BR122021016789B1 - HIV-1 VACCINES COMPRISING ONE OR MORE POPULATION EPISSENSE ANTIGENS, USES THEREOF TO PROTECT AN INDIVIDUAL FROM AN HIV-1 INFECTION, TREAT HIV-1 AND INDUCE AN EFFECTOR MEMORY T CELL RESPONSE, AS WELL AS POLYPEPTIDE AND METHOD FOR DESIGN AND PRODUCE SAID VACCINES - Google Patents

Abstract

The present invention relates to HIV-1 vaccines comprising a vehicle and a population episense antigen determined using the EpiGraph approach. HIV-1 vaccines are also provided that comprise a vehicle, a population episense antigen, and a personalized antigen. Also provided are methods for designing and producing an HIV-1 vaccine for an individual comprising designing vaccine antigens to ideally cover diversity within a geographic area using an amino acid sequence generated using the EpiGraph approach and producing said vaccine antigen. designed. Also provided are methods for inducing an effector memory T cell response comprising engineering the one or more EpiGraph amino acid sequences, producing a vaccine comprising the one or more EpiGraph amino acid sequences and a vector, and administering the vaccine to an individual. . Further provided are methods for treating HIV-1 in an individual comprising administering an effective amount of the described HIV-1 vaccines to the individual in need thereof.

Description

[001] Split from BR1120170068656, deposited on 10/05/2015.

REFERENCES TO RELATED DEPOSIT REQUESTS

[002] This application claims the benefit of priority to US Provisional Patent Application Serial No. 62/059,497, filed on October 3, 2014, and US Provisional Patent Application Serial No. 62/059,506, filed on October 3 2014, which is incorporated into this document, by way of reference in its entirety.

REFERENCE TO SEQUENCE LISTING SENT ELECTRONICALLY

[003] The content of the sequence listing sent electronically in ASCII text file (Name: 3525.010PC02 Seq listing_ST25.txt; Size: 3,634,253 bytes; and Creation Date: October 5, 2015) deposited with the application is incorporated in this document for reference in its entirety.

FIELD OF INVENTION

[004] The present subject relates, in general, to HIV and, in particular, to HIV vaccines.

BACKGROUND OF THE INVENTION

[005] In 2013, there were approximately 2.3 million new human immunodeficiency virus (HIV) infections, more than 35 million people living with HIV, and 1.6 million deaths from acquired immunodeficiency syndrome (AIDS). Although great progress has been made in treating HIV/AIDS, all individuals living with HIV will need to be treated with antiretroviral therapy (ART) for the rest of their lives, as drug therapy is unable to eliminate latent viral reservoirs existing in resting CD4 + T cells at a frequency of about 1/106 cells. See, Eriksson, S. 2013. PLoS Pathog 9:e1003174.

[006] The main strategies for purging latent HIV reservoirs are generally aimed at reactivating the latent virus using histone deacetylase (HDAC) inhibitors, however, clinical studies with HDAC inhibitors have not consistently decreased latent reservoirs. A likely reason for this lies in the inability of HIV-specific CD8+ T cells to eliminate resting CD4+ T cells.

[007] Only a few cases have been documented in which HIV-1 was eliminated from an individual with a pre-existing infection. Until an effective therapy is developed, the estimated 35 million individuals living with HIV-1 will remain on antiviral drugs to suppress a viral reservoir that has resisted all eradication efforts.

[008] A cure for AIDS has been elusive, but recent work suggests that strict immune control can eliminate HIV over time. Specifically, it was found that rhesus macaques (RM) vaccinated with cytomegalovirus (CMV)-based vectors expressing simian immunodeficiency virus (SIV) antigens were initially infected, but SIV was undetectable by several stringent criteria one to two years later. the infection. This result is even more considerable due to the fact that the highly virulent SIVmac239 strain used in these studies prevented previous vaccine attempts. These results have expanded the current paradigm from one focused on a preventive HIV vaccine to one in which immunotherapy for HIV/AIDS will eventually become an essential part of the fight against this pandemic. Therefore, in addition to a preventive vaccine, there is still a need for an effective therapy to treat individuals with HIV-1. Specifically, there remains a need to design, manufacture, and test prophylactic and therapeutic HIV vaccines in preparation for clinical trials.

SUMMARY OF THE INVENTION

[009] Provided herein are HIV/SIV polypeptides comprising one or more antigen sequences in the Epitope Graph (EpiGraph) comprising amino acid sequences corresponding to HIV/SIV Gag, Nef, Pol, Env, including sequences of length total, portions thereof, or any combination thereof. Provided herein are HIV/SIV polypeptides comprising one or more episense antigen sequences in the population comprising amino acid sequences corresponding to HIV/SIV Gag, Nef, Pol, Env or a combination thereof. Also provided herein are one or more carriers comprising HIV/SIV polypeptides comprising one or more episense antigen sequences in the population. Additionally provided herein are HIV/SIV polypeptides comprising one or more custom antigen sequences comprising amino acid sequences corresponding to HIV/SIV Gag, Nef, Pol, Env or a combination thereof. The HIV/SIV polypeptides of the present disclosure may comprise one or more HIV-1 personalized antigens, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 692 to 696 and SEQ ID NOs: 754 to 789. Also provided herein are one or more carriers comprising HIV/SIV polypeptides comprising one or more custom antigen sequences. EpiGraph antigen sequences having SEQ ID NOs: 691 to 789 are provided herein.

[010] Provided herein are vaccines against HIV-1 that comprise one or more vehicles and one or more episense antigens in the population. Also provided herein are HIV-1 vaccines that comprise a vector capable of expressing an episense antigen in the population and one or more personalized antigens.

[011] In some embodiments, the episense antigen in the HIV-1 population comprises epitopes of Gag, Pol, Nef, Env, Tat, Rev, Vpr, Vif or Vpu. In some embodiments, the episense antigen in the HIV-1 population is a fusion antigen comprising two or more episense antigens in the HIV-1 population. In some embodiments, the episense antigen in the HIV-1 population is essential for the HIV-1 clade B epidemic in the United States. In some embodiments, the episense antigen in the HIV-1 population is essential for the HIV-1 clade C in South Africa. In some embodiments, the episense antigen in the HIV-1 population is essential for the HIV clade 2 -1 regional epidemic in Thailand. In some embodiments, the episense antigen in the HIV-1 population is essential for the overall pool of HIV-1 group M.

[012] In some embodiments, the episense antigen in the HIV-1 population comprises Gag epitopes. In some embodiments, the episense antigen in the HIV-1 population comprises epitopes from a conserved region of HIV-1. In some embodiments, the episense antigen in the HIV-1 population comprises epitopes from a conserved region of Gag, Pol, or Nef. In some embodiments, the epitopes of the conserved region are epitopes of the Gag capsid protein p24.

[013] In some embodiments, the personalized HIV-1 antigen comprises Gag, Pol, Nef, Env, Tat, Rev, Vpr, Vif or Vpu epitopes. In some embodiments, the personalized HIV-1 antigen is essential for the global assembly of HIV-1 group M. In some embodiments, the personalized HIV-1 antigen is essential for epidemic HIV-1 clade C in South Africa. In some embodiments, the personalized HIV-1 antigen is essential for epidemic HIV-1 clade B in South Africa. U.S.

[014] Methods for preventing or treating HIV-1 infection in an individual are further provided which comprise administering an effective amount of the described HIV-1 vaccines to the individual in need thereof. Methods for designing and producing an HIV-1 vaccine for an individual are further provided which comprise sequencing HIV-1 viruses in an individual, selecting vaccine antigens designed to ideally cover density within a geographic area, and inserting the vaccine antigens into a vector. Also provided herein are methods for treating HIV-1 infection in an individual comprising administering an effective amount of the disclosed vaccines to the individual in need thereof.

[015] Also provided herein are HIV-1 vaccines that comprise one or more carriers and an episense antigen in the population determined using the Epitope Plot approach. Methods are further provided for designing vaccine antigens to ideally cover diversity within a geographic area using a vaccine antigen amino acid sequence generated using the EpiGraph antigen amino acid sequence selection method and producing the designed vaccine antigen. Further provided herein are methods for designing and producing an HIV-1 vaccine for an individual comprising determining the amino acid sequence of HIV-1 viruses in an individual by sequencing, selecting vaccine antigens designed to ideally cover the diversity within a geographic area using a vaccine antigen amino acid sequence generated using the Antigen Amino Acid Sequence Selection Epitope Plot method and inserting the vaccine antigens into a vector.

[016] Also provided are methods for inducing an effector memory T cell response comprising determining one or more EpiGraph amino acid sequences, generating a vaccine comprising the one or more EpiGraph amino acid sequences and one or more carriers, and administering the vaccine to an individual who needs it. Further provided are methods for treating HIV-1 in an individual comprising administering an effective amount of the described HIV-1 vaccines to the individual in need thereof. Also provided herein are methods for protecting against an HIV-1 infection in an individual comprising administering an effective amount of the described HIV-1 vaccines to the individual in need thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

[017] Figure 1A shows a complete graph for the CRF01-AE clade of the Nef protein. The rectangle is an inset shown in Figure 1B.

[018] Figure 1B represents the insertion of Figure 1A. Nodes are gray dots and represent each variant's k-repeat units, with k = 9. Edges are horizontal lines connecting epitopes whose sequences overlap by k - 1 amino acids, as shown in the first two epitopes (ea = VTSSNMNNA [SEQ ID NO: 790], and b = TSSNMNNAD [SEQ ID NO: 791]) on the top left side. Although the topological properties of the graph do not depend on node positions, this graph uses the vertical geometric axis to indicate the epitope frequency in the set of target sequences, y = f(e), for each node. The horizontal position x(e) = 1 + maxe'eP(e)x(e'), where P(e) is the set of predecessors of e, gives this graph the property that all directed edges connect to the left on the right. The ideal trajectory through this graph maintains as much as possible at the highest y values. The inset shows two trajectories through the nodes. The solid black line is the ideal trajectory, and corresponds to the sequence TSSNMNNADSVWLRAQEEE [SEQ ID NO: 792] while the dashed line corresponds to TSSNMNNNADCVWLRAQEEE [SEQ ID NO: 793]. The dashed line reaches higher f(e) values at 4 nodes, but the solid line has higher f(e) at 5 nodes, and ∑ f(e) is larger. Note that there is no trajectory that includes the nodes with the highest values for all x values.

[019] Figure 2 shows nodes of an epitope graph that shows the k epitope string, and the frequency (f) that the epitope is observed at the position in the set of aligned sequences, and the best cumulative score S of trajectories compatibles that end at that node. Nodes are arranged in columns with each column corresponding to the t position associated with the epitope. The lines connecting these nodes correspond to adjacent epitopes that are compatible. The objective is to find a compatible trajectory through this graph that maximizes the sum of frequency values at each node. The thicker lines show a trajectory that results in an ideal total score.

[020] Figure 3 shows that the initial solution nodes (provided by q1 = ARCHSLM [SEQ ID NO: 794] as shown in Figure 2 have their frequency values set to zero, and the cumulative scores S(t;e) are recomputed based on these new frequency nodes. This results in an optimal solution to this complementarity coverage problem: q2=DEFGKLM [SEQ ID NO: 795] The thicker lines show a trajectory that results in an optimal total score.

[021] Figures 4A to B show the epitope graph associated with a set of 690 US clade B Gag protein sequences [SEQ ID NOs. 1 to 690], each aligned to 556 positions. The horizontal axis is the t position, and the columns of nodes indicate the different epitopes at each position. The nodes are arranged so that the most frequent nodes in each position are at the bottom of each column. The complete graph is shown in Figure 4A; a close-up inset of the same graph is shown in Figure 4B.

[022] Figures 5A to C show that the exclusion of rare variants decreases coverage, but only slightly for Gag (Figure 5A), Nef (Figure 5B), and Pol (Figure 5C). Coverage of polyvalent solutions (m = 2) is shown as a function of minimum account fo (i.e., the population frequency of the rarest epitope in the vaccine). The dashed lines correspond to the coverage provided by the direct sequential algorithm; the solid black lines are based on the best solutions after 100 random restarts. The vertical axis, in all three graphs, is limited to a range of 0.015.

[023] Figures 6A to B show two-antigen vaccine coverage. Comparisons illustrating the average epitope coverage per sequence of contemporary clade B sequences isolated in the United States, which was considered a hypothetical target population for a therapeutic vaccine. To illustrate potential T cell epitope (PTE) coverage using a pair of natural sequences within the clade as vaccine antigens, 5000 randomly selected pairs of clade B natural sequences (gray) were evaluated as potential vaccines, and the distribution of Average coverage of the 189 contemporary clade B US sequences is shown in the gray histogram. This is compared to the average coverage provided by a set of 2 group M antigen Epitope Graphs (M database), a set of two global B clade EpiGraphs antigens (B database), and a personalized vaccine for clade B US in which the 2 best matches from a set of 6 representative epitope plots for manufacturing were selected as a “custom” match for each of the 189 natural clade B US sequences. Figure 6A shows the comparison of the full-length Gag protein. Figure 6B shows comparisons of only the conserved p24 region.

[024] Figure 7 shows the mapping of potential epitope coverage that spans the HIV proteome.

[025] Figure 8 shows the potential average Gag epitope coverage of U.S. HIV-1 clade B sequences by different vaccine antigens. Figure 8A shows the average Gag epitope coverage by individual vaccine antigens, and Figure 8B shows the average Gag epitope coverage by pairs of vaccine antigens.

[026] Figures 9A to C show that synthetic HIV antigens designed by Epitope Chart are expressed as full-length proteins. HeLa cells were transfected with expression plasmids encoding: gag and nef fusion proteins for HIV or SIV (HIV group M EpiGraph 1 [SEQ ID NO: 705] and HIV group M EpiGraph 2 [SEQ ID NO : 707], full-length SIVmac239 proteins, SIV variant hybrid proteins [SEQ ID NO: 713], and SIV conserved portions of gag and nef [SEQ ID NO: 714]), as depicted in Figure 9A; HIV or SIV polymerase proteins (SIVmac239 full length (FL), SIV variant hybrid proteins [SEQ ID NO: 715], (HIV group M EpiGraph 1 [SEQ ID NO: 709] and group M EpiGraph 2 of HIV [SEQ ID NO: 711], and SIV conserved portions of pol [SEQ ID NO: 716]), as depicted in Figure 9B; and gag and nef fusion proteins for HIV (EpiGraph 1 of clade B gag/nef [SEQ ID NO: 701]) and EpiGraph 2 of clade B gag/nef [SEQ ID NO: 702]) and HIV polymerase proteins (epi 1 of clade M pol [SEQ ID NO: 709]); Clade B pol EpiGraph 1 [SEQ ID NO: 703]); Clade B pol EpiGraph 2 [SEQ ID NO: 704]), as depicted in Figure 9C. All gag/nef constructs include a carboxy-terminal V5 tag (Figure 9A), and all pol constructs include a carboxy-terminal HA tag (Figures 9B and 9C). For Figure 9B, 1 and 2 indicate multiple clones of each construct. Lysates were harvested 48 hours after transfection and immunoblotted using V5 (Figure 9A) or HA (Figures 9B and 9C) antibodies. The observed molecular weight of the proteins is compatible with the predicted molecular weight for each of the constructs.

[027] Figures 10A to B show that synthetic antigens designed by EpiGraph are expressed by CMV vectors. As depicted in Figure 10A, full-length (FL) strain 68-1 RhCMV expression SIVmac 239 polymerase, a hybrid of SIV polymerases from different SIV variants [SEQ ID NO: 715], a synthetic polymerase gene based on Global group M HIV EpiGraph 1 [SEQ ID NO: 709] or global group M HIV EpiGraph 2 [SEQ ID NO: 711] were constructed by BAC mutagenesis and reconstituted in telomerized Rhesus fibroblasts. As depicted in Figure 10B, conserved regions of SIVmac239 expression and strain 68-1 RhCMV polymerase constructs [SEQ ID NO: 716] were also constructed by BAC mutagenesis and reconstituted in telomerized Rhesus fibroblasts. In all vectors, antigen expression is activated by the endogenous viral Rh107 promoter. Cell pellets were collected in complete CPE and immunostained for the HA tag expressed at the carboxy terminus of each protein. For conserved pol, two independent clones (2.1 and 2.2) are shown in Figure 10B.

[028] Figures 11A to C show conserved regions within: Nef (Figure 11A), Gag (Figure 11B), and Pol (Figure 11C) defined based on potential T cell epitope coverage (PTE) by a vaccine bivalent (i.e. 2 antigens).

[029] Figure 12 illustrates the average Epigraph coverage of each of the regions conserved by different vaccine antigens, compared to the more variable sections of the proteins.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[030] Various terms related to aspects of the description are used throughout the specification and claims. Such terms shall have their ordinary meaning in the art, except where otherwise indicated. Other specifically defined terms should be interpreted in a manner consistent with the definitions provided in this document.

[031] As used in this specification and the attached claims, the singular forms "a", "an" and "the" include plural referents except where the content clearly indicates otherwise. Thus, for example, reference to "a cell" includes a combination of two or more cells and the like.

[032] The term "about" as used herein when referring to a measurable value such as a quantity, a temporal duration, and the like, is intended to encompass variations of up to ± 20% from the specified value, since such variations are suitable for carrying out the disclosed methods. Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as molecular weight, reaction conditions and so on used in the specification and claims are to be understood as being modified in all cases by the term "about". Consequently, except where otherwise indicated, the numerical parameters presented in the following description and in the attached claims are approximations that may vary depending on the desired properties intended to be obtained by the present invention. At a minimum, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter must at least be interpreted in light of the number of significant digits reported and applying common rounding techniques.

[033] Although the numerical ranges and parameters that establish the broad scope of the invention are approximations, the numerical values presented in the specific examples are reported as accurately as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective test measurements.

[034] As used above and throughout the disclosure, the term "effective amount" refers to an effective amount, in dosages and for periods of time necessary, to obtain the desired result with regard to the treatment of the disorder, condition or relative side effect. It will be appreciated that the effective amount of components of the present invention will vary from patient to patient not only with the particular vaccine, component or composition selected, the route of administration and the ability of the components to obtain a desired result in the individual, but also with factors such as the state of the disease or the severity of the condition to be alleviated, the hormonal levels, the age, sex, weight of the individual, the condition of the patient and the severity of the pathological condition to be treated, simultaneous medication or special diets followed by the particular patient, and other factors that those skilled in the art will recognize, the appropriate dosage being at the discretion of the treating physician. Dosage regimens can be adjusted to provide improved therapeutic response. An effective amount is also one in which any toxic or harmful effects of the components are offset by the therapeutically beneficial effects.

[035] The term "administer" means directly administering a compound or composition of the present invention, or administering a prodrug, derivative or analogue that will form an equivalent amount of the active compound or substance within the body.

[036] The terms "subject", "individual" and "patient" are used interchangeably herein and refer to an animal, for example, a human being, to which treatment, including prophylactic treatment, with The pharmaceutical composition according to the present invention is provided. The term “individual” as used herein refers to human and non-human animals. The terms "non-human animals" and "non-human mammals" are used interchangeably herein and include all vertebrates, e.g. mammals, such as non-human primates (particularly greater primates), sheep, dogs, rodents (e.g. example, mouse or rat), guinea pig, goat, pig, cat, rabbits, cows, horses and non-mammals such as reptiles, amphibians, chickens and turkeys.

[037] The term "cocktail" refers to a set of antigens intended to be administered in combination to a patient.

[038] The term "episense" refers to an epitope-based consensus sequence. It is a sequence whose epitopes are compatible, as closely as possible, with the epitopes in a set of natural sequence references. The terms "epitope" and "potential epitope" refer to a sequence of k characters (typically k is in the range 8 to 12), often in the context of a k-character subsequence of a very large natural or vaccine antigen sequence. longer. T cells can recognize such peptides in an immune response.

[039] The term "EpiGraph" refers to a new computational strategy developed to create sequences that provide an ideal episense sequence, or set of sequences that combined provide ideal coverage of a population of diverse viral sequences.

[040] The terms "EpiGraph sequence" or "Epissenso antigen" refer to vaccine inserts designed based on the EpiGraph algorithm.

[041] The term "population episense antigen" refers to a sequence derived with the EpiGraph algorithm, which are "central" to a population of HIV sequences. The population could be a specific clade of HIV, a cluster of sequences derived using the custom epitope-based clustering algorithm, or the global epidemic. “Central” is defined in terms of potential epitope sharing, so it is a computationally derived sequence that provides the maximum population average epitope coverage.

[042] EpiGraph sequences could be used as a solution for a prophylactic preventive vaccine, or could be adopted as part of more complex strategies for designing therapeutic vaccines that could be personalized to match individual infections. The term "personalized vaccine set" refers to a set of vaccine antigen sequences designed for manufacturing, from which a subset of antigens could be selected to best match a patient's virus for administration as a therapeutic vaccine.

[043] The term "personalized antigen" or "personalized episense antigen" refers to one or more amino acid sequences from the "personalized vaccine pool" that could be specifically selected based on a best match to the HIV-1 strain infectious disease of a patient for administration to that patient as a therapeutic vaccine.

[044] As used herein, the terms "treatment" or "therapy" (as well as different forms thereof, including curative or palliative) refer to the treatment of an infected person. As used herein, the term "treatment" includes the alleviation or reduction of at least one adverse or negative effect or symptom of a condition, disease or disorder. This condition, disease or disorder may be HIV infection.

[045] As used herein, the terms "prevention" or "prophylaxis" refer to preventing an individual from becoming infected, or reducing the risk of an individual being infected, or stopping transmission, or reducing the risk of transmission , for example, from HIV, SIV or a related virus.

[046] “Pharmaceutically acceptable” refers to those compounds, materials, compositions and/or dosage forms that are, within the scope of medical judgment, suitable for contact with the tissues of humans and animals without excessive toxicity, irritation, response allergic or other complications of the problem compatible with a reasonable benefit/risk ratio.

[047] Vectors that can be used include, but are not limited to, plasmids, bacterial vectors and viral vectors. Viral vectors include cytomegalovirus (CMV) vectors. An advantage of these CMV vectors for use in the application of therapeutic vaccines is that they create a new CD8+ T cell epitope paradigm and induce more potent and long-lasting responses. It has been demonstrated in animal models that vaccines based on these viral vectors can eliminate viral infections (Hansen, SG 2013. Science 340: 1237874), and thus these approaches have the commitment of a therapeutic vaccine, a situation in which personalized vaccines can be Useful.

[048] Other viral vectors may include poxviruses (vaccinia), including vaccinia Ankara and canarypox; adenovirus, including adenovirus type 5 (Ad5); rubella; sendai virus; rhabdovirus; alphavirus; and adeno-associated viruses. Alternatively, EpiGraph vaccine antigens can be administered as DNA, RNA, or protein components of a vaccine. Because this is an antigen design strategy, vaccine antigens designed for EpiGraph could be compatible with virtually any mode of vaccine antigen delivery.

[049] In certain embodiments, vaccines designed using EpiGraph amino acid sequences have a single antigen. In certain embodiments, vaccines designed using EpiGraph amino acid sequences have sets of antigens.

[050] In certain embodiments, EpiGraph antigen sequences can be used in a prophylactic vaccine scenario.

[051] In certain embodiments, the EpiGraph strategy can be used to form sequences that completely optimize epitope coverage for a prophylactic vaccine. This could be one sequence, or several sequences designed to complement each other as a preventative vaccine. EpiGraph vaccines could be used in any vector, including, but not limited to, plasmids, bacterial vectors, and viral vectors.

[052] In the EpiGraph algorithm, natural sequences are characterized by a large graph of nodes, with each node corresponding to an epitope that appears in the natural sequences. Directed edges connect two nodes when the two corresponding epitope chains are “matched,” indicating that the last k-1 characters in the first chain match the first k-1 characters in the second chain (e.g., “EPTAPPAEPTAP” [ SEQ ID NO: 796] and “PTAPPAEPTAPP” [SEQ ID NO: 797] are supported k=12-repeat units). If two chains are compatible, then a chain of length k+1 (e.g., “EPTAPPAEPTAPP”) [SEQ ID NO: 798] contains both epitopes. More generally, a trajectory through this graph of nodes and edges corresponds to a single chain that contains subchains of k-repeat units corresponding to each of the nodes in the graph. Each node is weighted according to how many sequences in the reference set exhibit a substring corresponding to that node. The EpiGraph algorithm uses a dynamic programming scheme to find the trajectory through this complete graph that maximizes the sum of these weights and therefore provides the greatest coverage.

[053] Certain modalities provided include an HIV-1 vaccine comprising a vector and an episense antigen in the population, or combination of optimized EpiGraph antigens designed to be used as a set. There are many different vectors that could be used for the vaccine. For example, a type of vector that can be used in a viral vector. These viral vectors may include a human cytomegalovirus (HCMV), a poxvirus, adenovirus, rubella virus, sendai virus, rhabdovirus, alphavirus, or adeno-associated virus. The vaccine could also be delivered as a gene encoding the EpiGraph protein, using DNA, RNA, or included as an expressed protein or part of a protein.

[054] In certain embodiments, the EpiGraph antigen of the disclosed vaccines may be derived from the HIV-1 Gag protein. In another embodiment, the HIV-1 Gag protein was inactivated by eliminating a myristoylation sequence at the N terminus of the HIV-1 Gag protein. In another embodiment, the EpiGraph antigen may be derived from the HIV-1 Pol or Nef protein, or in fact any other HIV protein, including Env, Tat, Rev, Vif or Vpu.

[055] In certain embodiments, the episense antigen of the population can be determined using the EpiGraph approach. This population episense antigen could then be used to create a vaccine. Alternatively, EpiGraphs could be designed as a combination of sequences designed to be used as a set. HIV-1 can be divided into clades based on geographic location. In one embodiment, the population episense antigen is essential for the HIV-1 clade B epidemic in the United States in the disclosed vaccines. In another embodiment, the population episense antigen is essential for the HIV-1 clade C epidemic in South Africa in the disclosed vaccines. In another embodiment, the population episense antigen is essential for the regional HIV-1 clade 2 epidemic in Thailand in the disclosed vaccines. In another embodiment, the population episense antigen is essential for the global pool of HIV-1 group M in the disclosed vaccines.

[056] In some embodiments, the episense antigen in the HIV-1 population comprises epitopes of Gag, Pol, Nef, Env, Tat, Rev, Vpr, Vif or Vpu. In some embodiments, the episense antigen in the HIV-1 population comprises Gag epitopes and comprises the amino acid sequence of SEQ ID NO: 691, SEQ ID NO: 697, SEQ ID NO: 698, SEQ ID NO: 699, or SEQ ID NO: 700. In some embodiments, the episense antigen in the HIV-1 population comprises epitopes from a conserved region of HIV-1. In some embodiments, the episense antigen in the HIV-1 population comprises epitopes from a conserved region of Gag, Pol, or Nef. In some embodiments, the epitopes of the conserved region are epitopes of the Gag capsid protein p24.

[057] In some embodiments, the episense antigen in the HIV-1 population is a fusion antigen comprising two or more episense antigens in the HIV-1 population. In some embodiments, the fusion antigen comprises an episense antigen from the HIV-1 population comprising Gag epitopes and an episense antigen from the HIV-1 population comprising Nef epitopes. In some embodiments, the fusion antigen comprises an HIV-1 population episense antigen that comprises epitopes from a conserved region of Gag and an HIV-1 population episense antigen that comprises epitopes from a conserved region of Nef. In some embodiments, the conserved region fusion antigen epitopes are Gag p24 capsid protein epitopes.

[058] In some embodiments, the episense antigen in the HIV-1 population is essential for the HIV-1 clade B epidemic in the United States. In some embodiments, the HIV-1 population clade B episense antigen comprises Gag epitopes and comprises the amino acid sequence of SEQ ID NO: 730, SEQ ID NO: 732, or SEQ ID NO: 778. In some embodiments, The HIV-1 clade B population episense antigen comprises epitopes of the Gag capsid protein p24 and comprises the amino acid sequence of SEQ ID NO: 731, SEQ ID NO: 733, or SEQ ID NO: 779. In some embodiments, The HIV-1 population clade B episense antigen comprises Nef epitopes and comprises the amino acid sequence of SEQ ID NO: 734 or SEQ ID NO: 736. In some embodiments, the HIV-1 clade B population episense antigen 1 comprises epitopes from a conserved region of Nef and comprises the amino acid sequence of SEQ ID NO: 735 or SEQ ID NO: 737. In some embodiments, the HIV-1 population clade B episense antigen comprises Pol epitopes and comprises the amino acid sequence of SEQ ID NO: 703, SEQ ID NO: 704, SEQ ID NO: 738, or SEQ ID NO: 740. In some embodiments, the HIV-1 clade B population episense antigen comprises epitopes of a conserved region of Pol and comprises the amino acid sequence of SEQ ID NO: 739 or SEQ ID NO: 741. In some embodiments, the HIV-1 B clade population episense antigen is a fusion antigen comprising (1) an HIV-1 clade B population episense antigen comprising Gag epitopes and (2) an HIV-1 clade B population episense antigen comprising Nef epitopes, wherein the fusion antigen comprises the amino acid sequence of SEQ ID NO: 701 or SEQ ID NO: 702. In some embodiments, the HIV-1 clade B population episense antigen is a fusion antigen comprising (1) an HIV-1 clade B population episense antigen. 1 comprising epitopes from the Gag capsid protein p24 and (2) an episense antigen from the HIV-1 clade B population comprising epitopes from a conserved region of Nef.

[059] In some embodiments, the episense antigen in the HIV-1 population is essential for the HIV-1 clade C epidemic in South Africa. In some embodiments, the episense antigen of the HIV-1 population clade C comprises epitopes of Gag and comprises the amino acid sequence of SEQ ID NO: 742, SEQ ID NO: 744, or SEQ ID NO: 766. In some embodiments, the HIV-1 clade C population episense antigen comprises epitopes of the capsid protein p24 of Gag and comprises the amino acid sequence of SEQ ID NO: 743, SEQ ID NO: 745, or SEQ ID NO: 767. In some embodiments, the HIV-1 population clade C episense antigen comprises Nef epitopes and comprises the amino acid sequence of SEQ ID NO: 746 or SEQ ID NO: 748. In some embodiments, the HIV-1 clade C population episense antigen comprises epitopes from a conserved region of Nef and comprises the amino acid sequence of SEQ ID NO: 747 or SEQ ID NO: 749. In some embodiments, the HIV-1 population clade C episense antigen comprises Pol epitopes and comprises the amino acid sequence of SEQ ID NO: 750 or SEQ ID NO: 752. In In some embodiments, the HIV-1 clade C population episense antigen comprises epitopes from a conserved region of Pol and comprises the amino acid sequence of SEQ ID NO: 751 or SEQ ID NO: 753. In some embodiments, the episense antigen of HIV-1 clade C population B is a fusion antigen comprising (1) an HIV-1 clade C population episense antigen comprising Gag epitopes and (2) an HIV clade C population episense antigen -1 comprising Nef epitopes. In some embodiments, the episense antigen of the HIV-1 clade C population is a fusion antigen comprising (1) an episense antigen of the HIV-1 clade C population comprising epitopes of the Gag capsid protein p24 and (2) ) an episense antigen from the HIV-1 clade C population that comprises epitopes from a conserved region of Nef.

[060] In some embodiments, the episense antigen in the HIV-1 population is essential for the regional HIV-1 clade 2 epidemic in Thailand. In some embodiments, the HIV-1 clade 2 population episense antigen comprises Gag epitopes. In some embodiments, the episense antigen of the HIV-1 clade 2 population comprises epitopes of the Gag capsid protein p24. In some embodiments, the HIV-1 clade 2 population episense antigen comprises Nef epitopes. In some embodiments, the HIV-1 clade 2 population episense antigen comprises epitopes from a conserved region of Nef. In some embodiments, the HIV-1 clade 2 population episense antigen comprises epitopes from Pol. In some embodiments, the HIV-1 clade 2 population episense antigen comprises epitopes from a conserved region of Pol. HIV-1 B clade 2 population episense antigen is a fusion antigen comprising (1) an HIV-1 B clade 2 population episense antigen comprising Gag epitopes and (2) an HIV-1 B clade 2 population episense antigen comprising Gag epitopes. HIV-1 clade 2 comprising Nef epitopes. In some embodiments, the HIV-1 clade 2 population episense antigen is a fusion antigen that comprises (1) an HIV-1 clade 2 population episense antigen that comprises Gag p24 capsid protein epitopes and (2) ) an episense antigen from the HIV-1 clade 2 population that comprises epitopes from a conserved region of Nef.

[061] In some embodiments, the episense antigen in the HIV-1 population is essential for the global pool of HIV-1 group M. In some embodiments, the HIV-1 group M population episense antigen comprises Gag epitopes and comprises the amino acid sequence of SEQ ID NO: 718, SEQ ID NO: 720, or SEQ ID NO: 754. In some embodiments, The HIV-1 group M population episense antigen comprises epitopes of the Gag capsid protein p24 and comprises the amino acid sequence of SEQ ID NO: 719, SEQ ID NO: 721, or SEQ ID NO: 755. In some embodiments, The HIV-1 group M population episense antigen comprises Nef epitopes and comprises the amino acid sequence of SEQ ID NO: 722 or SEQ ID NO: 724. In some embodiments, the HIV-1 group M population episense antigen 1 comprises epitopes from a conserved region of Nef and comprises the amino acid sequence of SEQ ID NO: 723 or SEQ ID NO: 725. In some embodiments, the HIV-1 B group M population episense antigen is a fusion antigen comprising (1) an HIV-1 group M population episense antigen comprising Gag epitopes and (2) an HIV-1 group M population episense antigen comprising Nef epitopes, wherein the fusion antigen comprises the amino acid sequence of SEQ ID NO: 705 or SEQ ID NO: 707. In some embodiments, the HIV-1 B group M population episense antigen is a fusion antigen comprising (1) a population episense antigen of HIV-1 group M population comprising epitopes from the Gag capsid protein p24 and (2) an HIV-1 group M population episense antigen comprising epitopes from a conserved region of Nef, wherein the fusion antigen comprises the amino acid sequence of SEQ ID NO: 706 or SEQ ID NO: 708. In some embodiments, the HIV-1 group M population episense antigen comprises Pol epitopes and comprises the amino acid sequence of SEQ ID NO: 709, SEQ ID NO: 711, SEQ ID NO: 726, or SEQ ID NO: 728. In some embodiments, the HIV-1 group M population episense antigen comprises epitopes from a conserved region of Pol and comprises the amino acid sequence of SEQ ID NO: 710, SEQ ID NO: 712, SEQ ID NO: 727, or SEQ ID NO: 729.

[062] In certain embodiments, the disclosed vaccines may additionally comprise an HCMV vector comprising an HCMV backbone and a custom antigen selected to be a natural best match HIV-1 strain. In another embodiment, the disclosed vaccines may further comprise an HCMV vector comprising an HCMV backbone and a custom antigen selected to be a different best-match HIV-1 strain.

[063] In some embodiments, the personalized HIV-1 antigen comprises Gag, Pol, Nef, Env, Tat, Rev, Vpr, Vif or Vpu epitopes. In some embodiments, the personalized antigen comprises a sequence selected from: SEQ ID NOs. 692 to 696; SEQ ID NOs. 756 to 765; SEQ ID NOs. 769 to 777; or SEQ ID NOs. 780 to 789.

[064] In some embodiments, the personalized HIV-1 antigen comprises Gag epitopes and comprises the amino acid sequence of SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694, SEQ ID NO: 695, or SEQ ID NO: 696.

[065] In some embodiments, the personalized HIV-1 antigen is essential for the global pool of HIV-1 group M. In some embodiments, the HIV-1 group M personalized antigen comprises Gag epitopes and comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 756 to 765. In some embodiments, the group M personalized antigen HIV-1 M comprises epitopes of the Gag p24 capsid protein and comprises the amino acid sequence of SEQ ID NO: 757, SEQ ID NO: 759, SEQ ID NO: 761, SEQ ID NO: 763, or SEQ ID NO: 765 .

[066] In some embodiments, the HIV-1 personalized antigen is essential for the HIV-1 clade C epidemic in South Africa. In some embodiments, the HIV-1 clade C personalized antigen comprises Gag epitopes and comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 768 to 777. In some embodiments, the HIV-1 clade C custom antigen comprises epitopes of the Gag p24 capsid protein and comprises the amino acid sequence of SEQ ID NO: 769, SEQ ID NO: 771, SEQ ID NO: 773, SEQ ID NO: 775, or SEQ ID NO: 777.

[067] In some embodiments, the personalized HIV-1 antigen is essential for the HIV-1 clade B epidemic in the United States. In some embodiments, the HIV-1 clade B custom antigen comprises Gag epitopes and comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 780 to 789. In some embodiments, the clade B custom antigen HIV-1 B comprises epitopes of the Gag p24 capsid protein and comprises the amino acid sequence of SEQ ID NO: 781, SEQ ID NO: 783, SEQ ID NO: 785, SEQ ID NO: 787, or SEQ ID NO: 789 .

[068] In certain embodiments, methods of treating HIV-1 in an individual comprising administering an effective amount of one of the disclosed vaccines to the individual in need thereof. In another embodiment, selecting vaccine antigens to ideally cover diversity within a geographic area uses a vaccine antigen sequence generated using the EpiGraph antigen sequence selection method.

[069] Embodiments of the present invention include methods of treating HIV-1 infection in an individual that comprise administering an effective amount of any of these disclosed vaccines to the individual in need thereof.

[070] Embodiments of the present invention also include methods for inducing an effector memory T cell response comprising determining one or more EpiGraph sequences, generating a vaccine comprising the one or more EpiGraph amino acid sequences and vector, and administering the vaccine to an individual who needs it. In another embodiment, methods for inducing an effector memory T cell response are provided wherein the one or more EpiGraph amino acid sequences comprise SEQ ID NO: 697, SEQ ID NO: 698, SEQ ID NO: 699, or SEQ ID NO: 700. This vaccine can be a prophylactic or therapeutic vaccine.

[071] Recent advances in HIV vaccine research include the concept of an effector memory T cell (TEM) inducing vaccine to prevent HIV infection. Unlike central memory T cells (TCM) induced by traditional vaccine approaches, TEM are persistently maintained in lymphoid tissues and extralymphoid effector sites and are immediately ready to mediate antiviral effector function, thus providing constant immune protection at the portals of viral entry and viral reactivation sites. The vector system most qualified to induce and indefinitely maintain TEM is derived from CMV. Presumably due to continuous low-level reactivation and/or gene expression in persistently infected cells, CMV maintains just the right amount of persistent low-level immune stimulation required for maintenance of TEM without triggering T cell exhaustion.

[072] In certain embodiments, the personalized antigen cocktail can be used in a therapeutic vaccine scenario. For example, the personalized vaccine may use a k-means clustering strategy for a defined set of 6 to 10 sequences that provide very satisfactory epitope coverage in a population of people who are infected with a highly variable pathogen such as HIV. The virus infecting an individual can be sequenced and 2 or 3 personalized vaccines will be administered that best cover the infecting virus. Epitope coverage will be optimized while epitope mismatches will be minimized between the vaccine and the infecting strain.

[073] Certain embodiments provided include an HIV-1 vaccine comprising an HCMV backbone vector, which is devoid of certain CMV gene regions, and a population episense antigen. In certain embodiments, the HCMV backbone may be devoid of the UL131A-128 gene region. Certain embodiments may also include deletion of the pp71 tegument protein gene (UL82). (US Patent Application Publication Nos. 20140141038; 2008-0199493; 2013-0142823: and International Application Publication No. WO/2014/138209).

[074] In certain embodiments, the present disclosure provides vaccines that may comprise a second personalized antigen sequence. In certain embodiments, vaccines may comprise a second, third, or more personalized antigen sequences. The episense antigen may comprise the amino acid sequence of SEQ ID NO: 691. The personalized antigen may comprise the amino acid sequence of SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694, SEQ ID NO: 695 or SEQ ID NO: 696. In one embodiment, the first custom antigen sequence and the second custom antigen sequence comprise two of the amino acid sequences of SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694, SEQ ID NO: 695 and SEQ ID NO: 696. In another embodiment, the first custom antigen sequence, the second custom antigen sequence and the third custom antigen sequence comprise three of the amino acid sequences of SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694, SEQ ID NO: 695 and SEQ ID NO: 696.

[075] Custom antigen sequences are also provided that may comprise SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694, SEQ ID NO: 695 or SEQ ID NO: 696.

[076] In certain embodiments, the disclosed vaccines may additionally comprise an HCMV vector comprising an HCMV backbone and a custom antigen selected to be a natural best match HIV-1 strain. In another embodiment, the disclosed vaccines may further comprise an HCMV vector comprising an HCMV backbone and a custom antigen selected to be a different best-match (and distant) HIV-1 strain.

[077] In certain embodiments, the episense antigen and personalized antigen of the disclosed vaccines may be derived from the HIV-1 Gag protein. In another embodiment, the HIV-1 Gag protein was inactivated by eliminating a myristoylation sequence at the N terminus of the HIV-1 Gag protein. In another embodiment, the episense antigen and the personalized antigen can be derived from the HIV-1 Pol or Nef protein.

[078] In certain embodiments, methods of treating HIV-1 in an individual comprising administering an effective amount of one of the disclosed vaccines to the individual in need thereof. In another embodiment, methods are provided for designing and producing an HIV-1 vaccine for an individual comprising sequencing HIV-1 viruses in an individual, selecting vaccine antigens designed to ideally cover density within a geographic area, and inserting the vaccine antigens in a vector.

[079] Certain modalities include methods of treating HIV-1 infection in an individual that comprise administering an effective amount of any of these disclosed vaccines to the individual in need thereof.

[080] The following examples are provided to describe the modalities described in this document in more detail. They are intended to illustrate, not limit, the modalities.

[081] All documents, patents and patent applications cited in this document are incorporated herein, by way of reference, and may be used in the practice of the invention.

EXAMPLES Example 1: Graphical model for optimal epitope coverage of aligned sequences.

[082] The existence of a set S = {s1 , s2 , . . . , sN } of N aligned sequences was assumed. Each sequence is a string of alphabetic characters (corresponding to the twenty amino acids, possibly plus some special characters corresponding to gaps, unknowns, and such). Since the sequences are aligned, they all have the same length T, and positions t = 1. . . T are well defined from sequence to sequence; sn [t] will be written as the t’th character in the n’th sequence. It is useful to introduce the notation s[t : u] for the subsequence of s that begins at position t and ends at position u.

[083] A potential epitope has been defined as a short sequence of k characters, typically 8 to 12. The epitopes of interest are subsequences of the sequences in S. In fact, a sequence s can be conceived as a list of epitopes: e1, . . . , eT -k+1, with et = s[t : t + k - 1]. Note, however, that for a list of epitopes that are associated with a sequence, it is necessary that the epitopes are compatible. Specifically, it is necessary for any adjacent pair et and et+1 that the last k - 1 characters of et agree with the first k - 1 characters of et+1; that is: et [2 : k] = et+1 [1 : k - 1].

[084] For each epitope e, a frequency f (e) with which it can be associated counts the fraction of sequences in S for the epitope to appear.

[085] For the general cocktail problem, a set of artificial sequences Q = {q1, . . . , qM } is necessary whose epitopes have useful properties. Let EQ be the set of all epitopes that appear in Q; that is: EQ = {e | e = qm [t : t + k - 1] for some choice of m, t}.

[086] In particular, those epitopes were designed to cover as much of the sequence set S as possible. The goal was to optimize the coverage score ∑ f (e) where the sum is more than e ∈EQ

[087] With M < N, and typically M « N, no epitope, in general, can be covered.

[088] For the aligned sequence problem, some simplifications can be made. In this case, each position in the alignment was treated as a different (but not independent) problem. The frequency function now depends on position: f(t, e) was the number of sequences in S so that e is the subsequence of k-repeat units that started at position t; thus, f (t, e) = ∑ I (e = sn [t : t + k - 1])

[089] where I is the indicator function: it is one if its argument is true, and it is zero otherwise. The EQ set can also be partitioned according to position in q sequences. Thus: EQ [t] = {e | e = qm [t : t + k - 1] for m}

[090] This allows the production of a coverage measurement for each position c[t] = ∑ eeEQ [t] f(t,e), from which a total coverage is given by c = ∑t c[t].

[091] For the trivial special case k = 1, the epitopes were just the amino acid characters. However, even if the problem was common to solve, the solution was still useful. For M = 1, the best solution is given by the consensus sequence, with q1 [t] selected to be the amino acid that is most common at position t. For M = 2, one can optimize coverage by assuming that q2 [t] is the second most common amino acid at position t. And so on for M major.

[092] For k > 1, the problem becomes non-trivial, as the epitopes overlap, and then each c[t] can no longer be independently optimized. The M = 1 case was called the “episense” problem, because it is like the consensus, except that it is a consensus of epitopes that was requested.

[093] In one example, the consensus and the k = 3 episense disagree: The consensus used the most popular letter in each position. Episense used the most popular “epitope”, which is a potential epitope of a 3-character string. Table 1 expands this example to illustrate overlapping epitope chains.

[094] Table 1: Six sequences and their associated k = 3 epitopes are shown. The bottom line shows the consensus sequences (formed from the most common character in each position) and the most common epitopes in each position. However, these epitopes (in particular, EFG and CHS) are incompatible with each other, so they cannot be combined in a single episense solution. In this case, the best episense score is given (although not exclusively) by the sequence ARCHSLM [SEQ ID NO: 794], which covers 1+1+2+2+3=9 out of 30 possible epitopes in the sequences. The consensus, ARCGSLM [SEQ ID NO: 799], covers 1+1+1+1+3=7. Note that an upper limit on this score can be obtained from the frequency of the most popular epitopes at each position: in this case, that gives 2+2+2+2+3=11

[095] Solving the episense problem. The M=1 case was addressed first, in which a single sequence q whose epitopes ideally cover the epitopes in a list of unaligned sequences S was requested. The EpiGraph algorithm under suitable assumptions achieves the optimal solution. In the comparisons, the consensus algorithm was also considered (very simple and fast) and the genetic algorithm optimization (very slow) as described in (Fisher, Nat Med. 2007 Jan;13(1):100-6, incorporated herein document, for reference purposes). The EpiGraph algorithm is illustrated in Figures 1A and 1B.

[096] Next, the problem of the most common vaccine cocktail, with M> 1, was considered and showed how the episense algorithm was modified for this most common problem.

[097] Figure 2 shows nodes of an epitope graph, where each node includes the k epitope string, and the frequency (f) that the epitope is observed at the position in the set of aligned sequences, and the best score cumulative S of compatible trajectories ending at that node. Nodes were arranged in columns with each column corresponding to the t position associated with the epitope. The lines connecting these nodes correspond to adjacent epitopes that were compatible. The objective is to find a compatible trajectory through this graph that maximizes the sum of frequency values at each node.

[098] The thicker lines in Figure 2 show a trajectory that results in an ideal total score. There will always be at least one such trajectory, but it may not be exclusive.

[099] The cumulative score S(t, e) was defined as the highest possible score starting at t = 1 and ending at the epitope and position t. It was observed that S(t = 1, e) = f (e) and that the values of t > 1 can be recursively computed: S(t, e) = f (e) + maxe' S(t - 1, e ' ), with e' ∈E(t-1,e)

[0100] where E (t - 1, e) is the set of epitopes at position t - 1 that are compatible with e, which is at position t. Having computed this cumulative score for all epitopes, the total score was found for the best trajectory as the maximum score in the last column: Smax = maxe S(T - k + 1, e). Furthermore, it can be operated backwards from this maximum to find the ideal trajectory: e*T -k+1 = argmaxe S(T - k + 1, e) e*t-i = argmaxe' S(t - 1 , e') with e'∈E(t-1,e* t)

[0101] The sequence e*1, e*2, . . . , e*T-k defined the sequence of epitopes compatible with the highest score. The episense string q is obtained by removing the first character of each epitope: q[t] = et*[1], and ending with the last epitope: q[T - k : T ] = e Tk [1 : k] .

[0102] The argmax operator may not have a unique value; if not then there will be several solutions to the episense problem, all of which are ideal in the sense of coverage.

[0103] Gaps. To align sequences, insertions and deletions have to be addressed and this introduces gaps in the aligned sequences. For example, the sequences ARCCDEGH [SEQ ID NO: 806] and ARCDEFGH [SEQ ID NO: 807] were best aligned as ARCCDE-GH [SEQ ID NO: 808] and ARC-DEFGH [SEQ ID NO: 809]. Placeholder epitopes were developed to address these gaps in the EpiGraph algorithm.

[0104] Position Marker Epitopes: The k = 3 epitopes were ARC, RCC, CCD, CDE, DEG, EGH and ABC, BCD, CDE, DEF, EFG, FGH respectively; however, when the epitopes were aligned by the first column, gaps need to be introduced in that list: ABC, BCC, CCD, CDE, DEG, EGH, -GH and ABC, BCD, CDE, -DE, DEF, EFG, FGH. The -GH and -DE chains were position marker epitopes. Placeholders are not counted in the coverage function; that is: f(t; -XY) = 0. However, they were still useful due to the fact that they could be used to define the consistency of adjacent epitopes.

[0105] For sequences without gaps, two adjacent epitopes were considered compatible if the last k - 1 characters of the first epitope agreed with the first k - 1 characters of the second epitope. Thus, ABC and BCD are compatible, but BCC and CDE are not. When gaps are introduced, then a pair is compatible if the second epitope starting with a gapped character is considered, and the remaining k - 1 characters match the last k - 1 characters of the last epitope. Thus, CDE and -DE are compatible.

[0106] For the “drop-in-place” algorithm, a “substrate” sequence that is generally considered the consensus sequence was used. Then, all epitopes in all positions were adopted and classified according to the form in which they appear. Starting from the least frequent epitope, each epitope was deposited on the substrate by replacing the characters on the substrate at positions [t: t + k - 1] with the characters on the epitope. When the most frequently occurring epitope was deposited on the substrate, one chain was used as the q episense solution. Since more frequent epitopes overwrite rarer epitopes, greater epitope coverage was achieved. And since a single q sequence is always updated, the final solution will be composed of compatible epitopes.

[0107] The algorithm may not be fully deterministic, as some epitopes may have identical frequencies, and if their positions are overlapping, then the final result may depend on the order in which they are deposited. In implementation, the order that the ranking algorithm awards is adopted, but there is an opportunity to randomize these orders and do multiple runs of the algorithm, with some runs possibly giving higher scores.

[0108] Heuristic “drop-in-place” algorithm. In this algorithm, a “substrate” sequence was adopted as the consensus sequence, but substrate selection rarely makes any difference. All epitopes in all positions were adopted and classified according to the form in which they appear. Starting from the least frequent epitope.

[0109] Each epitope was “deposited” on the substrate by replacing the characters on the substrate at positions [t : t + k - 1] with the characters on the epitope. When the most frequently occurring epitope was finally deposited onto the substrate, there was a chain that was used as the q episense solution. Since the most frequent epitopes overwrite the rarest epitopes, a large epitope coverage was obtained. Since a single q sequence was always being updated, the final solution was composed of compatible epitopes.

[0110] The algorithm may not be fully deterministic, as some epitopes may have identical frequencies, and if their positions overlap, then the final result may depend on the order in which they are deposited. In implementation, the order that the ranking algorithm awards is adopted, but there is an opportunity to randomize these orders and do multiple runs of the algorithm, with some runs possibly giving higher scores. The utility of this randomized multiple-run approach has not been investigated.

[0111] The solution depends only on the most frequent epitopes at each position, so, for example in Table 1, it will be a compatible combination of DEF, EFG, CHJ, HJL, JLM. If they are deposited in this order (the first four have frequency 2, the last one has frequency 3), DECHJLM [SEQ ID NO: 810] is obtained so that the score 0+0+2+2+3=7 exceeds the consensus, but is less than ideal. If they are deposited in the order HJL, CHJ, EFG, DEF, JLM, DEFGJLM [SEQ ID NO: 811] could be obtained with a score of 2+2+1+1+3=9, which is the ideal score for this example. These two solutions are illustrated in Figure 3.

[0112] The aligned vaccine cocktail problem (M > 1). In the original mosaic solution using genetic algorithm optimization, all M mosaic sequences are optimized at the same time.

[0113] Sequential solutions. One way to extend the M = 1 episense solutions to the M > 1 problem is to modify the algorithms to optimize full coverage in order to optimize complementary coverage. That is: given a solution of episodes q1, find q2 that covers as many of the remaining epitopes as possible, not covered by q1.

[0114] Iterative refinement of sequential solutions. Given the initial solutions qi, q2,..., qM, a new estimate for qi can be recomputed. This is done by starting with the original frequency values for each of the epitopes, but setting to zero those epitopes that are covered by q2,..., qM. Optimizing this complementary coverage problem results in new qi. You can go through all the initial solutions this way, each time optimizing the complementary coverage.

[0115] Off-by-one scoring. The analysis shown so far values coverage only if an epitope in a sequence s is exactly matched by an epitope in a sequence q. But particularly for longer epitopes, e.g. k = 12, an epitope in a sequence may still be effective if it is a close match. For example, a concordance in ii of i2 characters may constitute satisfactory coverage.

[0116] Results. These algorithms were compared using a dataset of 690 sequences.

[0117] Figure 4 illustrates what the graph would look like for such a large data set. Figure 4 shows the graph associated with a data set of 690 US clade B Gag protein sequences [SEQ ID NOs. 1 to 690), each aligned to 556 positions. The results are shown in Table 2. The horizontal axis is the t position, and the columns of nodes indicate the different epitopes at each position. The nodes were arranged so that the most frequent are at the bottom. Nodes and edges (indicating compatibility of adjacent nodes) are shown. The complete graph is shown in (a); a close-up inset of the same graph is shown in (b).

[0118] Table 2 shows a comparison between coverage scores; this is the fraction of the epitopes (k = 12) in the S sequences that are covered (by exact match) by the epitopes in the vaccine sequences Q = {qi,...,qM}. TABLE 2

[0119] For the global EpiGraph solutions, the best EpiGraph sequences were determined based on group M, clade B, and clade C database sequences (including up to approximately 2015), as well as the second complementary EpiGraph sequence for a vaccine bivalent for Gag, Pol and Nef. An innovative advantage of the EpiGraph code over the mosaic design is that it allows for the deliberate exclusion of rare epitopes, a feature included in the design of the new sequences. See the figure below for an example of the impact of excluding rare group M variants. Figure 5A C illustrates the final EpiGraph values and Custom vaccines that were used.

Example 2: Graphical model for optimal epitope coverage of misaligned sequences.

[0120] A set S = {s1 , s2 , . . . , sN } of N unaligned protein sequences is adopted to characterize the variability of a virus over a target population (e.g. a phylogenetic clade, national or global). A potential epitope is a subsequence of k amino acids (typically k = 9). Each potential epitope, e, is assigned an integer frequency f(e) corresponding to the number of sequences in S in which e appears. The monovalent problem is to design a single artificial sequence q that resembles a natural protein but ideally covers the potential epitopes in population S. Writing E(q) as the set of epitopes that appear in q, the coverage measurement is

[0121] The numerator is the sum of the frequencies of epitopes appearing in q, and the denominator is normalized by the sum across all epitopes appearing in any of the sequences in S. This formulation can be expressed as a directed graph. Each node in the graph corresponds to a different epitope, and a directed edge connects two epitopes of length k (ea; and b) if those epitopes overlap by k-1 characters. A trajectory through the graph is a sequence of nodes ei, 62, ..., 6L, with an edge from ei to eM for i = 1, ..., L-1. This trajectory corresponds to a sequence of L+k-1 characters, which is the artificial antigen q.

[0122] If this directed graph has no cycles, then EpiGraph finds a trajectory through the graph that rigorously maximizes coverage, providing the optimal solution. Furthermore, this optimization is done with computational effort that scales only linearly with the size (as measured in nodes and edges) of the graph. In practice, the directed graph created from S may not be acyclic, although it often almost is, especially for larger values of k. For this case, the graph was “uncycled” by iteratively identifying cycles and then removing low-value edges until there were no cycles.

[0123] A multipurpose “cocktail” of m > 1 antigens can be created by running EpiGraph sequentially, and optimizing complementary epitope coverage. This is accomplished by treating the epitopes that were included in the first antigens as if their frequencies were zero and then running Epigraph on those modified frequencies. If any of the epitopes on the first antigens are required to complete a trajectory (and generate a complete protein), they will still be available, but they will be disadvantaged, as they no longer contribute to the coverage score. This sequential solution can be improved using iterative refinement.

Example 3: Personalized therapeutic vaccines.

[0124] Although it is not feasible to construct a vaccine designed for every individual, it is feasible to sequence that individual's virus to attempt to obtain a satisfactory match from within a small reference set of vaccine options. We first considered a US-based clade B test population, focusing on the Gag protein. A South African-based reference vaccine pool and a global vaccine pool were designed, as well as an updated US-based clade B design. p24 is the most highly conserved subprotein in Gag and can be excised from the larger Gag protein to provide a conserved region ~230 amino acids in length. A conserved region approach has also been considered as an alternative to Gag, perhaps focusing on regions in Gag and Pol, possibly including the conserved extension of Nef as well as any other proteins of interest.

[0125] This is a very different optimization question than trying to design a set that provides optimal population coverage for a prophylactic vaccine. In the prophylactic case, it is not known which viruses may be encountered by the vaccinated person. In therapeutic case, the infecting viral sequence can be obtained and combined.

[0126] The optimization was done considering two things: first, maximizing a subject's infecting virus matches and, second, minimizing mismatches so that the vaccine response is as targeted as possible on relative epitopes.

[0127] The phylogeny within the main HIV clades tends to have an unclear structure. Instead, it is a “starburst” with very long outer branches, and very short, ill-defined inner branches near the base. Part of this structure is likely due to intra-subtype recombination. Although difficult to quantify, recombination is certainly occurring relatively frequently and, by analogy with what is seen in terms of inter-subtype recombination, is likely to be extensive. Given the structure of the tree, simply using clustering on a phylogenetic tree to define the reference set of potential vaccines will not be as effective, as associations within the clade have limited meaning from an "epitope perspective". Instead, sequence relationships should be considered by relative measurement, and the reference set should be selected based on potential epitope similarities between natural strains and putative vaccine designs.

[0128] 12-repeat units were optimized considering class II epitopes, however the code can use any length k-repeat units as a reference point, where k is the supposed potential epitope length. 9-repeat units were also used. In previous work with mosaics, the ideal solution for 9-repeating units was almost ideal for other nearby lengths (8, 10, 11, 12), and is expected to carry over to the new algorithms described here. 9 repeat units were used for certain sets of personalized vaccines disclosed herein.

[0129] Ideally it was defined in terms of coverage of k-repeat units. This is defined by replacing each sequence with an “epitope bag”, that is, an unordered list of all k-repeat units that appear in the sequence. An epitope bag can be defined for a set of sequences by making a list of all k-repeat units that appear in any of the sequences in the set. The coverage of a given sequence S by a set of sequences Q={qi,q2,...,qN} is given by the fraction of epitopes in the bag of S that are also in the collective bag of sequences Q, where Q must be a multipurpose combination in a vaccine cocktail. This coverage has been optimized. Another quantity of interest was the fraction of epitopes in the Q bag that are not in the S bag. Although not (currently) used directly in optimization, a smaller fraction of these foreign epitopes are preferred, and these numbers are calculated for comparisons and experimental design.

[0130] Six (6) ways of finding “core sequences” were evaluated when performing clustering for a Custom vaccine incorporated into the Custom vaccine analysis code (see below). An EpiGraph solution was considered best, and was used for the final code. Various clustering strategies were also tested.

[0131] Here are the strategies tested to define central cluster sequences based on amino acids: 1) Consensus: Consensus was a common standard, obtained by concatenating the most common amino acid in an alignment. Based on Potential Epitope (k-repeat units): 2) Episense: This approach resolves a single core sequence within a population or within a cluster. Two algorithms were tested to find episense. The first is the drop-in-place algorithm. This starts with consensus as a “substrate”. Excluding very rare k-repeat units (those that are only found 1 time in the population), start with rare low-frequency variants and replace the consensus k-repeat units with the rare variant, then continue substituting with variants, moving up in the list of all k-repeat units based on their frequency, replacing and overwriting with increasingly frequent variants until the most frequent variants in k-repeat units are allowed to “stand”; overlapping k-repeat units with higher frequency naturally tend to replace overlapping peptides with lower frequencies. The second algorithm is EpiGraph, the same as described in Example 1. Epigraph sequences are calculated faster than GA mosaics, and thus were readily incorporated into a clustering algorithm required to design a personalized vaccine. In an experiment with a set of 690 aligned sequences of 556 amino acids comprising the Gag protein (SEQ ID NOs: 1 to 690), the EpiGraph solution was very close to a consensus, and was also very close to the single best mosaic, with only a difference in amino acids from the other two centroids. 3) Sequential: This approach solves a set of N sequences of vaccine options. Here, the episense is defined first for the population, and that is q1. Then, all k-repeat units that are already covered by q1 are deleted and the approach solves the second sequence in the series by the same drop-in-place process, to produce q2. Then, all k-repeat units already covered by q1 and q2 are deleted and the approach solves for q3 and so on until resolved to a set of N sequences, each including increasingly rarer versions of the potential epitopes. 4) Iterative: This is an iterative version of the sequential algorithm. It also produces a set of N sequences of vaccine options, in general, with better coverage than the sequential approach, but without the preferential ordering that the sequential algorithm produces. Starting with a sequential solution qi, q2, ..., qN, all epitopes that are in the sequence data set are identified, and then epitopes that are covered by q2, ..., qN are excluded. By resolving the episense using the remaining (non-deleted) epitopes, a new value is obtained for qi. The next step does the same with q2, deleting the epitopes on qi, q3, ., qN. And so on for q3 to qN. 5) Mosaic (GA mosaic): defined using the original genetic algorithm (GA). Mosaic refers to the genetic algorithm called Mosaic and/or antigen sequences produced by GA. Here, a set of mosaics of size N is solved for all at once, or the single best mosaic can be solved for, fixed, and solved for a complementary set of 5 to form a total of 6 vaccine option sequences. This strategy was employed to allow direct comparisons with clustering strategies described below. 6) More natural: This approach solves a set of N vaccine option sequences. The natural strain in a set is identified as most “epitope-centric,” that is, has the most common k-repeat units. To find the same, for each k-unit repeat in a given natural strain, a frequency can be assigned to that specific form based on its frequency in the population, and then sum the frequencies as a measure of how well the natural strain covers the population. The natural strain with the highest score is the best single strain, Nat.i. Then, the k-repeat units that are covered by Nat.i can be eliminated from the scoring scheme and the best complement to Nat.2 can be selected by finding the best natural strain for epitope coverage excluding the epitopes already covered by Nat. .i. This is done iteratively, then k natural strains are collected, where k is the number of vaccine options one wishes to consider, and they are ordered, so Nat.i is the best single strain, Nat.2 the best complement for Nat.i, Nat.3 the best complement to (Nat.i + Nat.2).

[0132] The vaccine options that have been explored are designed according to the following general strategies, comparing new ideas to specifically address therapeutic vaccine population sequences that have been designed in the past to optimize population coverage.

[0133] If all individuals were to receive the same vaccine (this might work better only with conserved regions), sequencing and personalization are not done - these are universal designs, not optimized for each individual:

[0134] Consensus: Find a single universal sequence that best covers the population. Candidates for this 1-universal sequence included: a population consensus, the best single GA mosaic, the episense, and the most "epi-centric" natural strain.

[0135] EpiGraph: Find 2 or 3 sequences based on the population and grant them to everyone in the population. This population-based strategy was compared using the GA mosaic, best natural strains, and the sequential and iterative mosaic solution. Since EpiGraphs are now available, and an improvement over Mosaics as you can also exclude rare epitopes, you can use them.

[0136] In contrast, for a personalized vaccine, each individual could obtain only the vaccine sequences that best matched their infection: Manufacture, for example, 6 vaccine antigen sequences, and choose the best one, or the best combination of 2 or 3 out of these 6 for application to the patient; that is, choosing those that provide the best coverage of a patient's infecting strain, with the fewest incompatible epitopes. Several strategies for this scenario were explored. a.Clustering sequences with a k-means-like strategy to create 6 clusters, 1,500 iterations were done (each of these iterations was a test splitting and merging step followed by some regular iterations) for the final sets, centroid sequences defined from these 6 groupings for vaccine sets. The distance between two sequences was defined as one minus the epitope coverage of one sequence by the other sequence. Initially, 6 randomly selected natural strains were used to produce the clusters. This provided a very highly related set of 6 centroid sequences. It was found that if more natural diversity was represented, this would create a better set of reagents to create tailored vaccines. Next, the 6 clusters were produced with most of the 6 natural strains (Nat6) complementary as these are very distinctive, and then reassigned to the center based on the clusters like episense, and iteratively regrouped and re-centered. This strategy was compared starting from the top 6 natural strains and using a consensus as the cluster centroid instead of episense, and episense gave slightly better coverage. Imposing a minimum cluster size also provided slightly better coverage (1, 5, and 20 as minimum cluster sizes were tested), so a minimum cluster size was incorporated as a constraint. A minimum size of 20 was better than 1 or 5. To implement a minimum size, if in a given cycle the number of sequences in a cluster size falls below the minimum size, the members of this "very small cluster" are reassigned to the best centroid of the other five clusters. To make a new cluster to replace what was lost, the cluster that has the greatest average distances to its centroid was divided taking into account two random natural sequences within the cluster as centroids and reforming two clusters on them, recalculating the centroids and moving on to the next step with these new six clusters. The centroids of these clusters were very close to the center of the tree. It was determined from the sequences that this is due to the consensus replicating repeatedly within the clusters that dominate the signal. b.Epissenso + (5 cluster centers). Here, the core sequence was first defined for the entire population using the EpiGraph algorithm (the population episense), fixed for inclusion as a vaccine reagent. Any epitopes matching the population episense were excluded from grouping considerations. Sequences are clustered as before, with a minimum size, but this time 5 clusters based on all potential epitopes except those found in the episense, so the clusters complement the population episense, were targeted. This was determined to be the best solution for Gag. By including the population's episense in each individual's personalized vaccine, even if a given most common k-repeat unit is not evident in their sampled HIV sequences, it may be camouflaged or a common form for reversion, given the frequent HIV amino acid that alternates between common forms. The second complementary sequence from one of the 5 clusters could then add to the variant a potential cross-reaction between the vaccine and the infecting strain. c.Define best EpiGraph, add 5 tessellation complements to get a set of six (the 5 added are not ordered), or define best natural, add 5 naturals in series.

[0137] After extensive comparisons and refinements, the use of the EpiGraph algorithm was favored to define the center of clusters for personalized vaccines. A set of 6 Gag protein antigens is provided for manufacturing in a custom model, which targets a global group M vaccine, a contemporary clade B vaccine, and a contemporary clade C vaccine for Southern Africa. Comparison of natural contemporary clade B sequence coverage using 2 natural clade B sequences, group M EpiGraphs, clade B EpiGraphs, or custom clade B is shown in Figure 6A to B; custom clade B designs provide the best epitope coverage.

[0138] The various scenarios can be summarized with a few numbers as noted in Table 3, which are triggered by M, C, T, A and P. These are described below in terms of the number of "pills" (i.e. antigens of vaccine) for each category: M=Manufactured, total number of pills created, from which some subset is selected for each individual. (Typically assumes M=6 or less). C=Common, those pills that everyone administers, possibly plus some custom pills. T/A=Personalized/Alternative, T is the number of personalized pills (among A alternatives) that are given to each individual, possibly in combination with some common pills. P=Per-individual total (T+C), the number of pills given to each individual. TABLE 3

[0139] In Table 3, the single underlined numbers indicate that, on average, more than 60% of the 12-repeat units in the natural sequences are covered by the vaccine (SATISFACTORY), while the double underlined numbers indicate that more than 70% of the 12-repeat units on average are not present in natural strains. C6-epi 2 0 2/6 6 1+5-Epi-C5 2 0 2/6 6

[0140] Custom - select best 1 of 6 for each of 690 population sequences: Not much better (0.54 vs 0.51) than just doing one for the entire population, but C6-epi is the best of the bunch class if 6 vaccines that would be made, and administer one of the six to an individual based on their sequence.

[0141] Hybrid Custom Pair: Set population center, add 1 of 5 centroids to best complement a fixed sequence to cover each of the test sequences -

[0142] Three best hybrids - define the center of the population, and 2 of 5 centroids to best complement a fixed sequence to cover the test sequence.

[0143] Common: Everyone receives the same vaccine based on population, or 1 or 2 vaccine antigens are administered:

[0144] Exact match 1+5-Epi-C5:

[0145] And off-by-one considered a 1+5-Epi-C5 correspondence:

[0146] ** these are probably the best solution. A population episense was made, the 12-repeat units found in the episense for clustering were excluded. When the population episense is fixed and the best episense from the other 5 complementary clusters is chosen to pair with it, the same response is obtained as when the best pair among the 6 variants was chosen. This means that the population episense has always been one of the best pairs.

[0147] Off by one: For the above estimates, only perfect matches were considered, for an epitope match between a vaccine cocktail and a natural strain, a perfect match of 12/12 was required. Mismatches are often well tolerated, particularly for class II epitopes; if a match requires 11/12 agreement, a mismatch is 10/12 or less. The truth is probably somewhere in between, and 10/12 may also be acceptable in some cases. Here, the best option is compared to a best natural strain option, with perfect matches:

[0148] Perfect match (extracted from the table above):

[0149] And off-by-one considered a correspondence:

[0150] Three pills, one common (same for everyone). And two custom pills, the best pair of the remaining five.

Example 4: Design and optimization of a “custom” antigen cocktail for HIV-1 clade B.

[0151] HIV diversity at the population level begins with rapid evolution within each infected host. Much of the diversity within the host is a direct consequence of immune escape (Bar, K. J. 2012. PLoS Pathog 8:e1002721., Liu, M. K. 2013. J. Clin. Invest. 123:380 to 93, and escape variants soon emerge after infection (Fischer, W. 2010. PLoS One 5:e12303). The goal of prophylactic vaccines is to quickly eliminate the infecting strain or prevent it from infecting initially. Since it is not known which strain will be transmitted, prophylactic vaccines must induce immunological responses that are active against any variant that may be encountered. In contrast, an immunotherapy can be directed against a known viral population present in a given host. Prophylactic and therapeutic vaccines against HIV must therefore be designed taking into account these distinct requirements. As illustrated in Figure 7, the mosaic solutions approximate the maximum possible epitope coverage for a given HIV population. The figure also reveals differences in the conservation of HIV proteins, with large segments of Gag, Nef and Pol being highly conserved, whereas most of Env as well as most of the small auxiliary proteins (data not shown) are highly variable. Although mosaics offer a near-ideal solution for epitope coverage in a population for a prophylactic vaccine, they do not exploit the additional information to know the sequence of the infecting strain targeted in a therapeutic setting.

[0152] Implementing a personalized vaccine design strategy requires manufacturing a manageable number of vaccine reagents that maximally capture the epitope diversity of the target population, sequencing HIV from the infected vaccine recipient, and then selecting among the vaccine reagent group from the subset of antigen insertions that best matches the individual. In this way, the personalized vaccine strategy is conceptually different from the mosaic vaccine model.

[0153] 98% of approximately 150,000 HIV sequences that have been sampled in the U.S. are clade B. US sampled clade B Gag B sequences, currently available from the Los Alamos HIV database, were used. There were 690 intact Gag sequences in this set (SEQ ID NOs. 1 to 690), each derived from a different infected individual, representing a cross-section of the diversity of US HIV strains. To maximize T cell epitope coverage in a hypothetical vaccine, while defining the number of different Gag sequences that need to be contained in a vaccine cocktail, an innovative computational strategy that couples the use of an algorithm epitope-based consensus sequence (or “episense”) with k-means-like clustering. Unlike a simple consensus sequence, which adopts the most common amino acid in each alignment position, episense searches for the most common epitope (e.g., 12-repeat units) starting from each alignment position. However, one cannot simply adopt the most common epitope at each position, as epitopes overlap, and this can lead to conflicts in nearby amino acids. The goal is to address these conflicts in a way that leads to maximum epitope coverage of a population by a vaccine.

[0154] To define a small set of antigens for manufacturing that represents the diversity of epitopes in the population, a k-means-like approach was used to partition the 690 Gag sequences into distinct clusters based on similarity of epitopes and sequences Separate episense sequences were generated for each cluster to serve as the cluster's core sequence. Manufacturing coverage of individual variant levels after 5 to 6 pools, and 6 vaccine vectors with 6 HIV antigen variants is feasible, so that a pool of 6 antigens is initially targeted. The algorithm starts with 6 randomly selected natural strains as initial centroid sequences, and assigns each of the remaining sequences to whichever of the 6 is closest. Within each of the 6 clusters, a new centroid sequence is computed, based on the episense of the sequences in that cluster. Then, all sequences are reassigned according to which of the new centroids is closest. This process converges to a k-means-like optimization for the design of the 6 vaccine antigens, which are adopted as the episense centroids of the individual clusters, and these antigens could be used as a manufactured set, from which to select those that provide the best match for a given vaccine.

[0155] A hybrid approach was found to substantially improve epitope coverage while minimizing increases in potential vaccine-specific responses. In the hybrid strategy, the core sequence was computed for the entire population (the episense population), and subsequent clustering was based exclusively on epitopes that were not found in the core sequence. In this way, cluster episense sequences complement the population epsisense. In this way, the 6-sequence reagent pool consists of a population episense and five complementary cluster centroid sequences, and individuals could receive a personalized two-antigen vaccine, the population episense paired with the best complementary sequence. This strategy produced more diverse sequences in the reference set and improved the potential coverage of natural Gag sequences in the test population as noted in Table 4.

[0156] Table 4. Average coverage by strain of potential epitopes in US clade B Gag by different vaccines

[0157] A personalized vaccine, design with 2 or 3 antigens, was manufactured for each of the 690 variants, selected from the population episense and the 5 complementary sequences derived from the cluster. This was compared with the potential epitope coverage of population-based vaccine strategies, where each vaccinee could receive the same vaccine, in mosaic or natural-best combinations. "Administered" indicates the number of antigens that could be included in a vaccine cocktail. “Manufactured" indicates the size of the reference group of vaccine antigens that would need to be synthesized to choose between the personalized approach to be used. The "% compatible" indicates the average number of perfectly compatible potential epitopes between each of the natural Gag variants and the vaccine; the higher this value, the more likely vaccine responses will show cross-reactivity with natural variants The "% mismatch" represents the fraction of potential epitopes in the vaccine that are not found in a given natural Gag sequence, calculated for each of the 690 sequences separately. then the average is calculated. The higher this value, the greater the vaccine's potential to elicit vaccine-specific responses that may deviate from cross-reactive responses. The enhancement factor indicates the increase in coverage using the proposed new vaccine model options rather than using a best natural single strain.

[0158] Custom vaccine solutions optimized on 12-repeat units are almost ideal for 9-repeat units, and vice versa, so clusters based on 12-repeat units should work well for class I epitope presentation and class II as seen in Table 5.

[0159] Table 5. Allowing a single amino acid mismatch when evaluating 9 repeat units or 12 repeat units to be considered as a positive match when calculating the average coverage of a 2-protein custom model

[0160] Finally, the personalized vaccine approach theoretically achieves optimal results if 1 out of 12 mismatches are tolerated in potential epitopes, rather than requiring identity (Table 5); Given this more lenient and perhaps more biologically realistic measure, approximately 90% of vaccine responses to personalized vaccines may show cross-reactivity with epitopes on compatible natural Gags. The personalized vaccine approach was superior to population mosaics, consensus sequences, and best natural strains in terms of both maximizing epitope coverage of Gag sequences and minimizing potentially harmful vaccine-specific epitopes (Figure 8). The code can also be applied to personalized vaccines using multiple sequences rather than using a representative of infected individuals and the application of the personalized vaccine model strategy to different populations (the epidemic clade C in South Africa, the regional epidemic clade 2 in Thailand, and global M group set) is explored.

[0161] Personalized vaccine antigens can provide better coverage (compared to population-based antigens) of natural sequences when the infecting strain is known.

Example 5: Double expression vectors

[0162] Using the population episense antigens and/or the custom antigens described herein, dual expression vectors are generated, with each expressing a full-length Gag antigen and a second HIV antigen. The second HIV antigen can be, for example, a fusion protein of reverse transcriptase (RT) and the central part of Nef. Integrase is not included, as it is a rather poor stimulator of T cell responses. Using CMV vectors (e.g., RhCMV or HCMV vectors) as dual expression vectors, it is possible to simultaneously induce T cells on two SIV or HIV antigens. many different.

[0163] For example, panels of up to six HCMV vectors containing custom Gag sequences based on the developed EpiGraph algorithm are generated (one vector expressing a Gag population episense antigen and five vectors expressing a Gag population-based Gag antigen). complementary cluster) and antigen panels covering RT and the central region of Nef are also designed. A vector expressing a Gag population episense antigen plus two vectors each expressing a different Gag antigen can be selected from the five cluster-based complementary antigens. These vectors can also contain one of two complementary HIV-1 EpiGraph RT/ nef sequences. When customization is not expected to improve coverage due to high conservation of these sequences, the 2-tile solution is retained and used for the vector. For example, one RT/nef mosaic is included in the population episense vector and the other is used in the custom vectors. A panel of HCMV-based vaccine vectors that can enter vaccine production is generated by sequencing the resulting vectors and characterizing them for antigen expression and in vitro growth.

[0164] DNA inserts optimized for synthetic codons are generated corresponding to the Gag, RT and Nef mosaic and the custom antigens designed in Example 3.

Example 6: Temporary expression of viral antigens developed using the EpiGraph approach.

[0165] Antigens designed to maximize epitope frequency using the EpiGraph algorithm resemble natural sequences, but no longer encode native proteins. Although theoretical guidelines for the expression of these artificial sequences are adhered to in the construction of these sequences, the proteins encoded by them may exhibit unanticipated expression profiles or may not express a stable full-length protein.

[0166] To evaluate the expression profile of these sequences in the context of mammalian cells, EpiGraph sequences were synthesized and cloned for temporary transfection. DNA encoding these constructs was synthesized (Genscript, Piscataway, NJ) to contain compatible cloning sites for plasmid vectors (pcDNA3.1 and pOri). All inserts were optimized for the respective host (rhesus, SIV or human, HIV). Each construct was also modified to eliminate residual enzymatic activity from the native sequence as described in Kulkarni et al. Vaccine (2011). Deleted positions were based on the amino acid sequence relative to Clade B EpiGraph-1. Deleted amino acids include; "DTG" associated with protease activity (positions 81 to 83), "YMDD" associated with reverse transcriptase activity (positions 338 to 341), "E" associated with RNaseH activity (position 633), "D" 779), "D" associated with Integrase activity (position 831), and "E" associated with Integrase activity (position 867). Synthetic DNA was rehydrated in water and digested with restriction endonucleases (5' NheI, 3' BamHI) followed by heat inactivation. The plasmid vector was linearized with compatible endonucleases and treated with calf intestinal phosphatase to prevent recircularization of the empty vector. The vector and insert fragments were resolved by agarose gel electrophoresis to confirm digestion fragment sizes and cleaned for ligation by PCR purification kit (Thermo Scientific). The inserts were ligated into a linearized vector at an insert to vector ratio of about 3:1 for 15 minutes at room temperature using a rapid ligation kit (Roche, Indianapolis, IN), transformed into E. coli (DH5-alpha ) chemically competent and placed on antibiotic selection plates. DNA from the resulting colonies was screened by insertion restriction digestion

[0167] Clones containing each of the correct insertions in the appropriate orientation relative to the vector promoter and poly (A) sequences were grown in liquid culture for plasmid DNA purification. Subconfluent Hela cells actively growing in 12-well tissue culture plates received 500ul of fresh medium (DMEM 10% FBS) while liposomes were prepared. To generate liposomes containing plasmid DNA, 250 μl of serum-free medium was mixed with 500 ng of plasmid DNA and 250 μl of serum-free medium was mixed with 2 μl of lipid (Lipofectamine 2000, Invitrogen). After 5 minutes of incubation at room temperature, these solutions were combined, mixed and incubated for 20 minutes. The DNA-containing liposomes (500 ul) formed during this process were added dropwise to the culture and allowed to incubate for 12 to 16 hours, after which the transfection mixture was replaced with fresh medium. After an additional day of incubation, cultures were harvested by scraping and centrifugation. Supernatants were removed by aspiration and cell pellets were lysed by resuspension in 100ul gel loading dye containing 5% SDS and 10% 2-mercaptoethanol and centrifugation through a QiaShred column (Qiagen, Valencia, CA).

[0168] Expression of EpiGraph proteins was demonstrated by SDS-polyacrylamide gel electrophoresis (SDS-page) and by Western blotting developed with antibodies to the V5 or hemagglutinin epitope tag manipulated in each construct. Briefly, 10% polyacrylamide gels were prepared and loaded with 10 µl (10% of each sample) and electrophoresed at 110 to 120 volts for 90 minutes. Resolved proteins were transferred to PVDF membranes by semi-dry blotting at 20 volts for 45 to 50 minutes. Nonspecific binding was blocked with a solution of 10% skimmed milk powder in phosphate-buffered saline with 0.1% tween-20 (PBS-T) for 60 minutes. Antibodies to HA (Sigma) or V5 (Santa Cruz) were diluted in 5% milk solution and incubated with membranes for 1 hour followed by 3 washes with PBS-T before adding 1:2000 dilution of anti-Sigma secondary antibody. goat mouse conjugated with horseradish peroxidase (Santa Cruz) for 1 hour. Subsequently, the blots are washed three times in PBS-T and developed with enzyme-linked chemiluminescence (ECL) kit (Thermo-Pierce) and visualized with X-ray film.

[0169] All tested constructs demonstrated robust temporary expression of proteins of the predicted molecular weight and confirmed their usefulness for testing on the CMV vector backbone. (e.g., see Figures 9A to C).

Example 7: Engineering of EpiGraph-designed antigens into CMV vector BAC constructs and expression of reconstituted viruses.

[0170] EpiGraph antigens were designed to maximize coverage of T cell epitopes representative of the spectrum of viral sequences and HIV clades from which they were generated. To utilize these antigens more effectively, they were engineered into CMV vectors that demonstrated three times the CD8+ T cell spectrum of competing platforms. The broad antigen presentation and lifelong expression profiles of CMV vectors have demonstrated the ability to protect and cure SIV-infected rhesus macaques. The EpiGraph antigen design algorithm in combination with CMV vectors can provide even greater coverage of HIV within and across clades when applied to broadly prophylactic vaccines or personalized targeted vaccines.

[0171] EpiGraph sequences that were demonstrated to be expressed in temporary transfection systems were subcloned into the recombination plasmid (pOri) and transferred into CMV backbones using BAC recombination. (Messerle et al. Proc Natl Acad Sci U S A. 1997 Dec 23;94(26):14759 to 63; and Borst et al. J Virol. 1999 Oct;73(10):8320 to 9).

[0172] BAC recombination facilitates the manipulation of large DNA sequences using temperature- and metabolite-regulated recombination enzymes in the context of the E. coli strain EL250 containing a parental BAC. Recombination is a two-step sequential process consisting of insertion of the antigen sequence with an antibiotic resistance gene (kanamycin) into the target region followed by removal of the kanamycin cassette. The insertion fragments are amplified by PCR from template DNA containing the antigen of interest plus kanamycin using primers with long homology arms (50+ bp).

[0173] To prepare the bacterial cells for the insertion step, five ml cultures were grown overnight at 30°C in Luria Broth (LB) with chloramphenicol and diluted to 50 ml the next morning. The bacteria were grown for approximately 3 to 4 additional hours at 30°C (to an OD = 0.6) and then heat shocked by shaking at 42°C for 15 minutes to induce recombination enzymes. After this induction, the bacteria were pelleted (3000 rpm, 10 minutes, 4°C) and then washed three times in ice-cold water. E. coli cells became electrocompetent to receive the PCR product and recombination competent to insert the sequence into the target region of the BAC. The purified insert (500 ng) was combined with 100 μl of competent E. coli on ice, moved to a 0.2 cm crucible (Fisher), and electroporated using the Bio-rad MicroPulser apparatus. After electroporation, bacteria were diluted by adding 900 μl of LB culture medium and allowed to recover at 30°C for 2 hours before plating on chloramphenicol/kanamycin plates. Plates were incubated at 30°C for two days and colonies were filtered by restriction digestion and PCR for recombination events.

[0174] Recombination-positive BAC constructs proceeded to the second step in which the kanamycin cassette was excised by arabinose induction of Flip recombinase mediated by flanking FRT sites. 5 ml cultures were grown overnight in LB + chloramphenicol and diluted 1:10 the next morning. After three hours of growth, the bacteria were treated with L-arabinose (Arcos, final concentration 0.1%) and induced for 1.5 hours at 30°C. After induction, the bacteria were smeared onto chloramphenicol plates and incubated for two days at 30°C. Colonies were then replicated onto chloramphenicol/kanamycin and chloramphenicol plates to analyze clones that had lost resistance to kanamycin. These clones were further analyzed by restriction digestion and PCR to confirm the construct.

[0175] Viral Reconstitution: To regenerate the virus, BAC DNA was transferred into mammalian host cells permissive for viral growth. BAC DNA purified from 10 ml of an overnight culture was electroporated into approximately 1/5 of a confluent flask of telomerized fibroblasts (~200,000 cells). Briefly, cells were pelleted (1,500 rpm, 5 minutes) and resuspended in 700 μl of Opti-Mem. This cell mixture was then added to 50 μl of BAC DNA and mixed gently before transferring to a 4 mm crucible. Electroporation was performed using the Bio-rad GenePulser II at 0.25 kV and 0.95 uF. After electroporation, cells were plated in 100 mm dishes containing DMEM + 10% FBS and the medium was changed the next day to remove cell debris. Cells were observed daily for plaque formation and harvested in complete CPE. The remaining bound cells were harvested by cell scraper and pelleted by centrifugation (1,500 rpm, 5 minutes), and the supernatant containing the reconstituted viral vector was retained for passage of the recombinant virus. Cell pellets were lysed by resuspension in 100ul gel loading dye containing 5% SDS and 10% 2-mercaptoethanol and centrifugation through a QiaShred column (Qiagen, Valencia, CA).

[0176] Viral EpiGraph Expression: Expression of EpiGraph proteins was tested by SDS-polyacrylamide gel electrophoresis (SDS-page) and by Western blotting developed with antibodies to the V5 or hemagglutinin epitope tag manipulated in each construct. Briefly, 10% polyacrylamide gels were prepared and loaded with 10 μl (10% of each sample) and electrophoresed at 110 to 120 volts for 90 minutes. Resolved proteins were transferred to PVDF membranes by semi-dry blotting at 20 volts for 45 to 50 minutes. Nonspecific binding was blocked with a solution of 10% skimmed milk powder in phosphate-buffered saline with 0.1% tween-20 (PBS-T) for 60 minutes. Antibodies to HA (Sigma) or V5 (Santa Cruz) were diluted in 5% milk solution and incubated with membranes for 1 hour followed by 3 washes with PBS-T before adding 1:2000 dilution of anti-Sigma secondary antibody. goat mouse conjugated with horseradish peroxidase (Santa Cruz) for 1 hour. Subsequently, the blots were washed three times in PBS-T and developed with enzyme-linked chemiluminescence (ECL) kit (Thermo-Pierce) and visualized with X-ray film.

[0177] All tested constructs demonstrated robust stable expression of proteins of the predicted molecular weight, thus confirming their usefulness for immunogenicity tests in the CMV vaccine model in rhesus. (for example, see Figure 10A to B).

Example 8 Epigraph Vaccines in the Population:

[0178] The Epigraph algorithm was used to create a set of vaccine antigens initially using CMV vectors, however, other vaccine delivery systems can be used.

[0179] Group M (global) was considered, as well as clade B and C (geographically limited use to regions where these particular clades are endemic). Epigraph vaccine antigens of Gag, Pol, and Nef were generated. Groups B and M are expressed.

Basic Epigraph Design Attributes:

[0180] Epigraphs use a graph theory/dynamic programming approach to design antigens that maximize potential T cell epitope coverage (PTE). Under certain conditions, they are mathematically ideal and are very computationally efficient. Epigraphs have an additional tangible benefit over Mosaic antigens in that the benefit of excluding increasingly rare epitopes in the constructs can be balanced by tolerating minimal PTE coverage costs. These Epigraphs were designed with this fact in mind, allowing for a slight coverage cost (0.005) to ensure that even the rarest epitopes represented in the Epigraph antigens were observed in many of the population sequences (the precise number depends on the input dataset).

[0181] The input data sets for these Epigraphs were obtained from the HIV database sequence alignment set for each of the proteins, Gag, Pol and Nef, including one sequence per person, circa Sep 2014. Incomplete sequences were excluded. This left the following sequence numbers for each set of proteins, Nseqs is the number of sequences in the input alignment

[0182] Paired Epigraph antigen sets for a bivalent vaccine were sequentially resolved using the Epigraph algorithm for unaligned sequences. The sequential solution was used, which allows the use of the first Epigraph as a monovalent vaccine in isolation. This means they are designed so that the best single Epigraph antigen, an “episense,” is resolved first to provide optimal PTE coverage of a population, and is then fixed for inclusion in the bivalent design. The complement is then resolved to provide the best population PTE coverage by a bivalent pair of antigens that contain the first Epigraph, the episense. Coverage costs were minimal relative to a simultaneous antigen solution.

[0183] An analysis was then performed to determine the coverage cost of excluding rare variants. The data is summarized in the following table. fo is the rare epitope threshold. Sequences are produced after discarding all that appear in fo or fewer sequences. In other words, each PTE that is in the vaccine appeared in more than four sequences. These fo values were the largest possible while achieving coverage that was within 0.005 of the maximum coverage achieved when fo=0. Nseqs is the number of sequences in the input alignment.

[0184] The basic Epigraph antigens were designed as complete proteins, and these were expressed in CMV vectors and tested as Gag/Nef or Pol fusion proteins with deletions made for safety or as the most conserved regions of Gag and Nef fused or the regions more conserved than fused Pol. Lists of each full-length protein form for expression in the CMV vector are included below with examples from group M and clade B.

[0185] The conserved regions for vaccine antigens are excised from the full-length Epigraph proteins.

[0186] The conserved regions within Gag, Pol and Nef were defined based on the potential for PTE coverage by a bivalent vaccine (i.e. 2 antigens). That is, they were based on the potential of two optimized antigens to provide clade B PTE coverage. The sequences for the conserved regions are shown in the list below. The boundaries were selected to capture the most conserved half of each of the three proteins (Gag, Pol, and Nef), in the longest possible contiguous fragment, so the conserved regions are interspersed with more variable sections. In Gag, the contours simply reflect the contours of the capsid protein p24.

Example 9: Personalized Therapeutic Antigens

[0187] For personalized antigens, Gag or the more conserved part of Gag, p24 were used. For one project, the 2015 complete M-group alignments of 4596 sequences were used, to provide a global solution. An alignment of 189 contemporary clade B sequences was isolated from the US, or an alignment of 199 contemporary clade C sequences from South Africa. "Contemporary" refers to viruses that were isolated after 2004; All sequences sampled over the past decade were used to obtain a reasonable sampling of sequences from each region. Sequences that were not fully resolved or were incomplete were excluded. Regional subtype-specific contemporary viruses were selected because they represent satisfactory matches for populations that would be likely for initial proof-of-concept studies to evaluate personalized vaccines; Using regional single-subtype pools, population diversity could be limited to increase the potential for success of a therapeutic HIV vaccine.

[0188] These therapeutic vaccine antigens are designed to be used in treatment scenarios where they could be matched, or “customized,” to the sequenced infecting virus of the person receiving the vaccine. 6 vaccine antigens could be manufactured, the best 2 or 3 matches from the pool to the individuals infecting virus could be given to an individual to maximize matches between the vaccine and its infecting strain.

[0189] Thus, the complete Gag for each epigraph is provided below, for manufacturing the custom 6-antigen solution, with p24 as in bold. Gag or the more conserved p24 could be used in a personalized vaccine.

[0190] Compatible PTE scores and incompatible scores (number of extras), for the distribution of the n best matching antigens from a group of m, for Gag proteins or the interior p24 region, where the n are selected to best cover each individual sequence in the target population. Target populations are the contemporary clade C-infected population sampled in South Africa, or the contemporary clade B population sampled in the USA. The best solutions use a group of m=6 antigens, and are in bold; these are based on the six sequences shown above.

[0191] South African Clade C Gag Epitope Coverage

[0192] South African clade C p24 Gag Epitope Coverage

[0193] US Clade B Gag Epitope Coverage

[0194] US Clade B p24 Epitope Coverage

Example 10: Vaccine Test

[0195] Vaccine ramifications for initial testing in CMV include: 1) A single population episense Gag antigen, essential for the US epidemic clade B; 2) Population episense plus a custom Gag protein selected to be a best-match natural HIV-1 strain; 3) Population episense plus a custom Gag protein selected to be a different (and distant) best-match natural HIV-1 strain; 4) Population episense plus both Gag proteins from cohorts 2 and 3. Resulting immune responses are analyzed using overlapping 15-repeat unit peptides (4 amino acid overlap) corresponding to the vaccine antigen (to determine specific specific responses vaccine-induced Gag sequences) and then to the “target” HIV-1 strain and selected non-target HIV strains (see below) to measure strain-specific responses and the level of epitope matching (comparing Gag sequences from HIV target vs. non-target). It was determined that computationally designed insertions and vector combinations provide greater magnitude and broader T cell responses to the target strain, while minimizing responses corresponding to the non-target strain. The results of this analysis allow us to experimentally test the epitope matching predictions generated in Example 1.

[0196] Four cohorts of 5 Rhesus Macaques (RM) are inoculated with 106 PFU of HCMV vectors as follows: cohort 1 receives a single vector containing the clade B episense sequence, cohort 2 receives the episense vector plus one single personalized vaccine vector, cohort 3 receives episense plus a different personalized vaccine vector, and cohort 4 receives episense plus both personalized vaccine vectors. The vaccines are "customized" to 2 representative transmitted/founder HIV strains selected from a small set of 9 clade B U.S. HIV infections that have been extensively sequenced longitudinally; this panel represents a spectrum of natural infection comparable to what would be found in a human clinical trial. Essentially, these two divergent natural strains are being used as prototypes by patients. The pair of vaccine insert insertion elements, which is optimized for one, will be suboptimal for the other and vice versa, allowing - through determination of cross-recognition to sets of peptides reflecting each strain-specific sequence - reciprocal analysis of the possibility that there is a benefit to the present custom sequence matching strategy. In addition to this reciprocal analysis, the sequence of the other 7 infections will vary in their "match" relative to the selected vaccine vector insertion element(s) and By analyzing the responses to sets of peptides that reflect the sequences of these other 7 HIV strains, the reaction between the vector insertion sequence and the vector combination in magnitude and breadth of compatible versus incompatible responses will be extensively analyzed. Part of the motivation for focusing on this set of 9 strains is that carefully sequenced full-length genomes are available from longitudinal samples. Isolates are also available as infectious molecular clones, which may be useful for evaluating responses in subsequent human studies. Thus, by doing the groundwork in MRI using this set, there will be a compatible set of proteins particularly useful for direct comparisons between macaque and human responses when these vaccines are advanced into human studies.

[0197] Rhesus monkeys (RM) are inoculated subcutaneously on day 0 and week 12 and followed longitudinally for one year. Since vaccination by HCMV vectors is not affected by pre-existing anti-RhCMV immunity, animals naturally infected with RhCMV are used for these experiments. Intracellular cytokine analysis by flow cytometry (ICS) is used to determine the response of CD4+ and CD8+ T cells to individual consecutive 15 repeat unit peptides comprising the vaccine sequences within the vaccine inserts administered to each animal (which will understand the total responses induced by the vaccine). It is then determined that these epitope-specific T cells recognize epitope variants in both the target strain and the other 8 non-target strains. For peptides that show responses to strain-specific epitopes, the magnitude, functional avidity and functional characteristics (production of IFN-γ, TNF-a, IL-2 and MIP-1β and externalization of CD107) of these responses to the peptide variants" parental” are compared to determine the degree of functional cross-reactivity. In selected cases, truncation analysis is used to identify the nuclear epitope for similar comparative analyses. To determine the percentage of MHC-II restricted CD8+ T cells present, mAbs " blockers" specific for MHC-I and MHC-II, and the invariant chain-derived MHC-II-specific binding peptide, CLIP, are used to inhibit influenza-specific CD8+ T cell responses in PBMC, as has been done previously for influenza-specific of SIV.

[0198] Regardless of T cell priming results related to vector-specific genes, immunological analysis allows testing the hypothesis that T cells induced by personalized vaccines are superior with respect to epitope coverage of a given natural HIV reservoir in compared to non-personalized vaccines. The custom 2-antigen cocktail could likely generate T cell responses with at least a 25% higher frequency of cross-reactive responses to their corresponding natural strain compared to episense individually (Table 5). A test was also done to determine whether including 3 complementary custom antigens in a cocktail induces more cross-reactivity or whether antigen dilution or the presence of a greater number of vaccine-specific epitopes required by adding 3 rather than 2 antigens actually decreases the magnitude or breadth of the response with cross-reactivity to the natural protein. CMV-based T cell responses are expected to be much broader and therefore cover a much greater percentage of sequences than previously reported for other vectors. Thus, even with a relatively small number of animals, there must be sufficient epitope responses to assess the impact of sequence variation on the cross-reactivity potential of responses. The number and magnitude of all vaccine responses are determined using sets of peptides corresponding to the vaccine. Once the targeted peptides are determined, using only those peptides that are positive in each animal, the impact of natural variation on each vaccine-responsive peptide is determined. The natural variants that are tested are based on the variation found in a reference panel, including both custom and mismatched Gags. Non-parametric statistical and computational resampling methods are used as the primary tools to evaluate the impact of epitope variation on magnitude reduction or recognition abrogation. These analyzes are complemented, however, by using generalized linear models as necessary to explore the impact of more complex interactions on T cell response cross-reactivity. SEQ ID NO: 691 Episense sequence of personalized vaccine antigens. MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEEL KSLYNTVATLYCVHQKIEVKDTKEALDKIEEEQNKSKKKAQQ AAADTGNSS QVSQNYPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQA AMQML KETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRM YSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQ GVGGPGHKARVLAEAMSQVTN-- SATIMMQRGNFRNQRKTVKCFNCGKE GHIARNCRAPRKKGCWKCGKEGHQMKDC--TERQANFLGKIWPSH- KGRPGNFLQ SRPEPT APPEESFRFGEETTTPS QKQEPIDKE LYP-LASLRSLFGNDPSSQ SEQ ID NO: 692 Custom Vaccine Antigen 1 Sequence. MGARASVLSGGELDKWEKIRLRPGGKKKYRLKHIVWASRELERFAVNPGLLETSGGCRQILEQLQPSLQTGSEEL RSLYNTVATLYCVHQKIDVKDTKEALEKIEEEQNKSKKKAQQ AAAAADTGNNS QVSQNYPIVQNMQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNSVGGHQ AAMQML KETINEEAAEWDRVHPVHAGPVAPGQMREPRGSDIAGTTSTLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRM YSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQ GVGGPSHKARVLAEAMSQATN-- SATIMMQKGNFRNQRKIVKCF NCGKEGHIAKNCRAPRKKGCWKCGREGHQMKDC--TERQVNFLGKIWPSH- KGRPGNFLQ NRPEPT APPAESFRFGEETTTPP QKQEPIDKE LYP-LASLKSLFGNDPSSQ SEQ ID NO: 693 Custom Vaccine Antigen 2 Sequence. MGARASVLSGGKLDKWEKIRLRPGGKKRYKLKHIVWASRELERFAVNPGLLETAEGCRQILGQLQPALQTGSEEL KSLFNTVATLYCVHQRIDVKDTKEALEKIEEEQNKSKKKAQP AAADTGSSS QVSQNYPIVQNMQGQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFAALSEGATPQDLNLMLNTVGGH QAAMQML KETINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKKWIIMGLNKIVRM YSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQ GVGGPSHKARVLAEAMSQATN-- SATIMMQRGNFKNQRKTIKCF NCGKEGHIAKNCRAPRKKGCWKCGREGHQMKDC--TERQANFLGKIWPSH- KGRPGNFLQ NRPEPT APPAESFRFGEETTTPP QKQEPIDKE LYP-LASLKSLFGNDPSSQ SEQ ID NO: 694 Custom Vaccine Antigen 3 Sequence. MGARASVLSGGELDKWEKIRLRPGGKKKYRLKHIVWASRELERFAVNPGLLETSGGCRQILEQLQPSLQTGSEEL RSLYNTVATLYCVHQKIDVKDTKEALEKIEEEQNKSKKKAQQ AAAAADTGNNS QVSQNYPIVQNMQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNSVGGHQ AAMQML KETINEEAAEWDRVHPVHAGPVAPGQMREPRGSDIAGTTSTLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRM YSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQ GVGGPSHKARVLAEAMSQATN-- SATIMMQKGNFRNQRKIVKCF NCGKEGHIAKNCRAPRKKGCWKCGREGHQMKDC--TERQVNFLGKIWPSH- KGRPGNFLQ NRPEPT APPAESFRFGEETTTPP QKQEPIDKE LYP-LASLKSLFGNDPSSQ SEQ ID NO: 695 Custom Vaccine Antigen 4 Sequence. MGARASVLSGGKLDKWEKIRLRPGGKKKYRLKHIVWASRELERFAVNPGLLETAEGCRQILGQLQPALQTGSEEL RSLYNTVATLYCVHQRIEVKDTKEALEKIEEEQNKSKKKVQQ AAAADTGNSN QVSQNYPIVQNIQGQMVHQPLSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTIGGHQ AAMQML KETINEEAADWDRLHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRM YSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQ GVGGPSHKARVLAEAMSQVTN-- SATIMMQKGNFRNQRKIVKCFNCG KEGHIAKNCRAPRKRGCWKCGKEGHQMKEC--TERQANFLGKIWPSY- KGRPGNFLQ SRPEPS APPEESFRFGEETATPS QKQEPIDKE LYP-LASLKSLFGNDPSSQ SEQ ID NO: 696 Custom Vaccine Antigen 5 Sequence. MGARASVLSGGKLDKWEKIRLRPGGKKQYKLKHLVWASRELERFAVNPGLLETAEGCRQILGQLQPALQTGSEEL KSLFNTVATLYCVHQRIDVKDTKEALEKIEEEQNKSKKKAQQ AAADTGNNS QVSQNYPIVQNIQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFSALAEGATPQDLNTMLNTVG GHQAAMQIL KETINEEAAEWDRLHPVQAGPVAPGQMREPRGSDIAGTTSNLQEQIAWMTHNPPIPVGEIYKRWIIMGLNKIVRM YSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQ GVGGPSHKARVLAEAMSQATN-- PATIMMQRGNFKNQRKIV KCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKEC--TERQANFLGKIWPSY- KGRPGNFLQ SRPEPS APPEESFRFGEETTTPP QKQEPIDKE LYP-LTSLRSLFGNDPSSQ SEQ ID NO: 697 Antigen Sequence EpiGraph 1. MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQIL GQLQPSLQTGSEEL KSLYNTVATLYCVHQRIDVKDTKEALDKIEEEQNKSKKKAQQ AAADTGNSS QVSQNYPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQML KETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPI PVGEIYKRWIILGLNKIVRM YSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQ GVGGPGHKARVLAEAMSQVTN-- SATIMMQRGNFRNQRKTVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDC--TERQANFLGKIWPSH- KGRPGNFLQ SRPEPT APPEESFRFGEETTTPS QKQEPIDKE LYP-LASLRSLFGNDPSSQ SEQ ID NO: 698 Cocktail Antigen 1 EpiGraph. MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEEL KSLYNTVATLYCVHQRIDVKDTKEALDKIEEEQNKSKKKAQQ AAADTGNSS QVSQNYPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQA AMQML KETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRM YSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQ GVGGPGHKARVLAEAMSQVTN-- SATIMMQRGNFRNQRKTVKCFNCGKE GHIARNCRAPRKKGCWKCGKEGHQMKDC--TERQANFLGKIWPSH- KGRPGNFLQ SRPEPT APPEESFRFGEETTTPS QKQEPIDKE LYP-LASLRSLFGNDPSSQ SEQ ID NO: 699 Cocktail Antigen 2 EpiGraph. MGARASVLSGGKLDKWEKIRLRPGGKKKYRLKHIVWASRELERFALNPGLLETAEGCRQILGQLQPALQTGSEEL KSLFNTVATLYCVHQKIDVKDTKEALEKIEEEQNKSKKKAQQ AAAAADTGNNS QVSQNYPIVQNMQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNLMLNTVG GHQAAMQIL KETINEEAADWDRLHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRM YSPVSILDIKQGPKEPFRDYVDRVYKTLRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQ GVGGPSHKARVLAEAMSQATN-- SATIMMQKGNFRNQRKIV KCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKEC--TERQANFLGKIWPSY- KGRPGNFLQ NRPEPT APPAESFRFGEETTTPP QKQEPIDKE LYP-LASLKSLFGNDPSSQ SEQ ID NO: 700 Cocktail Antigen 3 EpiGraph. ARASVLSGGELDKWEKIRLRPGGKKQYKLKHLVWASRELERFAINPGLLETSGGCRQILEQLQPSLQTGSEELRS LYNTVAVLYCVHQRIEVKDTKEALEKVEEEQNKSKKKVQQ AAADTGNSN QVSQNYPIVQNIQGQMVHQPISPRTLNAWVKVIEDKAFSPEVIPMFAALSEGATPQDLNTMLNTIGGHQ Aamqml REGHIAKNCRAPRKKGCWKCGREGHQMKDCTERQRQANFLGKIWPSS- KGRPGNFLQ SRPEPS APPEESFRFGEETATPS QKQEPIDKE LYP-LTSLRSLFGNDPSLQ SEQ ID NO: 701 HIV B gag/nef fusion Epigraph 1 MGARASVLSGGELDRWEKIRLRPGGKKKYRLKHIVWASRELERFAVNPGLLETSEGCRQILG TLQPSLQTGSEEL GEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRF YKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSAT IMMQRGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQ SRPEPTAPPEESF RFGEETTTPSQKQEPIDKELYPLASLKSLFGNDPSSQGGKWSKSSIVGWPAVRERMRRAEPA AEGVGAVSRDLEKHGAITSSNTAATNADCAWLEAQEEEEVGFPVRPQVPLRPMTYKGALDLSHFLKEKGGLEGLI YSQKRQDILDLWVYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVEPEKVEEANEGENNSLL HPMSQHGMDDP EKEVLMWKFDSRLAFHHMARELHPEYYKDC SEQ ID NO: 702 Epigraph 2 HIV gag/nef fusion TALSEGATPQDLNTMLNTIGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPV APGQMREPRGSDIAGTTSNLQEQIAWMTHNPPIPVGEIYKRWIIMGLNKIVRMYSPVSILDIKQGPKEPFRDYVD RFYRTLRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQVTNS ATI MMQKGNFRNQRKIVKCFNCGKEGHIARNCRAPRKRGCWKCGKEGHQMKECTERQANFLGKIWPSYKGRPGNF LQNRPEPTAPPAESFRFGEETATPPQKQEPIDKEMYPLASLRSLFGNDPSQGGKWSKRSVPGWNTIRERMRRTEP AAEGVGAASRDLERHGAITSSNTAANNAACAWLEAQEDEEVGFPVKPQVPLRPMTYKAAVDLSH FLKEKGGLEGL IHSQKRQEILDLWVYNTQGYFPDWHNYTPGPGTRFPLTFGWCFKLVPVDPEQVEKANEGENNCLLHPMSLHGMDD PEREVLVWKFDSRLAFHHVAREKHPEYYKDC SEQ ID NO: 703 HIV B Pol Epigraph 1 MFFRENLAFPQGKAREFSSEQTRANSPTRRELQVWGRDNNSLSEAGADRQGTVSFSFPQ ITLWQRPLVTIKIGGQ LKEALLADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCT LNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWR KLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTV LDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYN VLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPP FLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVVPLTEEAEL E LAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKIA TESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETK LGKAGYVTDRGRQKVVSLTDTTNQKTQAIHLAL FTST TVKAACWWAGIKQEFGIPYNPQSQGVVSMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSA GERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRDPLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDY GKQMAGDDCVASRQDED SEQ ID NO: 704 HIV B Pol Epigraph 2 MFFREDLAFPQGEAREFPSEQTRANSPTSRELQVWGGDNNSPSEAGADRQGTVSLSFPQITLWQRPLVTVKIGGQ LKEALLADDTVLEEMSLPGKWKPKMIGGIGGFIKVRQYDQVPIEICGHKTIGTVLIGPTPVNIIGRNLLTQLGCT LNFPISPIETVPVKLKPGMDGPRVKQWPLTEEKI KALIEICTEMEKEGKISRIGPENPYNTPIFAIKKKDSTKWR KLVDFRELNKKTQDFWEVQLGIPHPSGLKKKKSVTVLDVGDAYFSVPLDKEFRKYTAFTIPSTTNNETPGIRYQYN VLPQGWKGSPAIFQCSMTKILEPFRKQNPEIVIYQLYVGSDLEIGQHRAKIEELRQHLLKWGFTTPDKKHQKEPP FLWMGYELH PDKWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGAKALTEVIPLTKEAEL ELAENREILREPVHGVYYDPTKDLIAEIQKQGLGQWTYQIYQEPFKNLKTGKYARTRGAHTNDVRQLTEAVQKIT TESIVIWGKTPKFRLPIQKETWETWWTEYWQATWIPEWEFV NTPPLVKLWYQLEKEPIIGAETFYVDGASNRETK LGKAGYVTNRGRQKVISLTDTTNQKTLQAIYLALQDSGSEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIN KEKVYLAWVPAHKGIGGNEQVDKLVSTGIRKVLFLDGIDRAQEEHEKYHNNWRAMASDFNLPPIVAKEIVASCDK CQLKGEAIHGQVDC SPGIWQLCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFILKLAGRWPVKTVHTNGS NFTSATVKAACWWAGVKQEFGIPYNPQSQGVVSMNNELKKIIGQIRDQAEHLKTAVQMAVFIHNFKRKGGIGEYS AGERIIDIIATDIQTRELQKQITKIQNFRVYYRDNRDPLWKGPAKLLWKG EGAVVIQDNSEIKVVPRRKVKIIRD YGKQMAGDDCVAGRQDED SEQ ID NO: 705 HIV gag/nef fusion epigraph 1 QQAAADTGNSSQVSQNYPIVQNLQGQMVHQAISPR TLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAP GQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRF YKTLRAEQATQEVK NWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSAT IMMQRGNFKGQKRIKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQS RPEPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLKSLFGNDPLSQGGKWSKSSIVGWPAVRERMRRA EPAA EGVGAVSRDLEKHGAITSSNTAATNADCAWLEAQEEEEVGFPVRPQVPLRPMTYKGALDLSHFLKEKGGLEGLIY SKKRQEILDLWVYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVDPREVEEANEGENNCLLHPMSQHGMDDPE KEVLMWKFDSRLAFHHMARELHPEYYKDC SEQ ID NO: 706 Epigraph 1 conserved gag/nef of HIV M MPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETIN EEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVS ILDIRQGPKEPFRDYVDRF YKTLRAEQATQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGP GHKARVLVGFPVRPQVPLRPMTYKGALDLSHFLKEKGGLEGLIYSKKRQEILDLWVYHTQGYFPDWQNYTPGPGI RYPLTFGWCFKLVP SEQ ID NO: 707 HIV M gag/nef fusion Epigraph 2 MGARASVLS GGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETAEGCQQIIEQLQSTLKTGSEEL KSLFNTVAVLYCVHQRIDVKDTKEALEKIEEEQNKSQQKTQQAAAGTGSSSKVSQNYPIVQNAQGQMVHQPLSPR TLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNMMLNIVGGHQAAMQML KDTINEEAAEWDRVHPVHAGPIPP GQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIILGLNKIVRMYSPTSILDIKQGPKEPFRDYVDRF FKTLRAEQASQEVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQVTNSAT IMMQRGNFRNQRKTVKCFNCGKEGHLARNC RAPRKKGCWKCGREGHQMKDCNERQANFLGKIWPSNKGRPGNFPQ SRPEPTAPPAESFRFEETTPAPKQEPKDREPLTSLKSLFGSDPLSQGSKWSKSSIVGWPAIRERMRRTEPAAEGV GAASRDLERHGAITSSNTAANNADCAWLEAQEDEEVGFPVKPQVPLRPMTYKAAFDLSFFLKEKGGLDGLIYSQK RQDILDLWVYNT QGFFPDWQNYTPGPGVRYPLTFGWCFKLVPVEPEKVEEANEGENNSLLHPMSLHGMDDPEREV LMWKFDSSLARRHMARELHPEFYKDC SEQ ID NO: 708 Epigraph 2 conserved gag/nef of HIV M MPIVQNAQGQMVHQPLSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNMMLNIVGGHQAAMQMLKDTIN EEAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIILGLNKIVRMYSPTS ILDIKQGPKEPFRDYVDRFFKTLRAE QASQEVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGP SHKARVLVGFPVKPQVPLRPMTYKAAFDLSFFLKEKGGLDGLIYSQKRQDILDLWVYNTQGFFPDWQNYTPGPGV RYPLTFGWCFKLVP SEQ ID NO: 709 HIV Pol Epigraph 1 M MFFRENLAFPQGEAREFSSEQTRANSPTRRELQ VWGRDNNSLSEAGADRQGTVSFSFPQITLWQRPLVTIKIGGQ LKEALLADDTVLEDINLPGKWKPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLVGPTPVNIIGRNLLTQIGCT LNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWR KLVDFRELNK RTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYN VLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQLYVGSDLEIGQHRTKIEELRQHLLKWGFTTPDKKHQKEPP FLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKV KQLCKLLRGAKALTDIVPLTEEAEL ELAENREILKEPVHGVYYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKIA TESIVIWGKTPKFRLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETK LGKAGYVTDRGR QKVVSLTETTNQKTLQAIHLALQDSGSEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIK KEKVYLSWVPAHKGIGGNEQVDKLVSSGIRKVLFLDGIDKAQEEHEKYHSNWRAMASDFNLPPIVAKEIVASCDK CQLKGEAMHGQVDCSPGIWQLCTHLEGKVILVAVHVASGYIEAEVIPAETGQETA YFLLKLAGRWPVKVIHTNGS NFTSAAVKAACWWAGIKQEFGIPYNPQSQGVVSMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYS AGERIIDIIATDIQTKELQKQITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD YGKQMAGDDCVAGRQ DEDQ SEQ ID NO: 710 Epigraph 1 preserved from pol of HIV M MPQITLWQRPLVTIKIGGQLKEALLADDTVLEDINLPGKWKPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLV GPTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPE NPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPH PAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYT AFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQLYVGSDLEIGQHRTKIEELRQ HLLKWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYHGQVDCSPGIW QLCTHLEGKVI LVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKVIHTNGSNFTSAAVKAACWWAGIKQE FGIPYNPQSQGVVSMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIIDIIATDIQTKLQK QITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDIKVVPRR KAKIIRDYGKQMAGDDCVAGRQDEDQ SEQ ID NO: 711 HIV Pol Epigraph 2 M MFFREDLAFPQGKAREFPSEQTRANSPTRGELQVWGGDNNSPSEAGADRQGTVSFSFPQITLWQRPLVSIKVGGQ IKEALLADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLIGPTPVNIIGRNMLTQ LGCT LNFPISPIDTVPVTLKPGMDGPRVKQWPLTEEKIKALTEICKEMEKEGKITKIGPENPYNTPIFAIKKKDSTKWR KLVDFRELNKKTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTIPSTTNNETPGIRYQYN VLPQGWKGSPAIFQCSMTKILEPFRIKNPEIVIYQLYVGSDLEIGQ HRAKIEELREHLLRWGFTTPDKKHQKEPP FLWMGYELHPDRWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYAGIKVRQLCKLLRGTKALTEVVPLTEEAEL ELAENREILKTPVHGVYYDPSKDLVAEIQKQGQGQWTYQIYQEPYKNLKTGKYARKRSAHTNDVRQLTEVVQKIA TESIVI WGKTPKFKLPIQKETWEAWWTDYWQATWIPDWEFVNTPPLVKLWYQLEKDPIVGAETFYVDGAASRETK LGKAGYVTNRGRQKVVSLTDTTNQKTLHAIHLALQDSGLEVNIVTDSQYALGIIQAQPDRSESEVVNQIIEELIK KEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGID KAQEEHERYHSNWRTMASDFNLPPVVAKEIVANCDK CQLKGEAIHGQVDCSPGMWQLCTHLEGKIILVAVHVASGYMEAEVIPAETGQETAYFILKLAGRWPVKTIHTNGS NFTSTTVKAACWWAGIQQEFGIPYNPQSQGVVSMNNELKKIIGQVREQAEHLKTAVQMAVFIHNFKRRGGIGGYS AGERIVDIIATDI QTRELQKQIIKIQNFRVYYRDSRDPLWKGPAKLLWKGEGAVVIQDNSEIKVVPRRKVKIIKD YGKQMAGDDCVASRQDED SEQ ID NO: 712 Epigraph 2 conserved from HIV M pol MPQITLWQRPLVSIKVGGQIKEALLADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLI GPTPVNIIGRNMLTQLGCTLNFPISPIDTVPVTLKPGMDGPRVKQWPLTEEKIKALTEICKEMEKEGKITKIGPE NPYNTPIFAIKKKDSTKWRKLVDFRELNKKTQDFWEVQLGIPHPAGLKK KKSVTVLDVGDAYFSVPLDESFRKYT AFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRIKNPEIVIYQLYVGSDLEIGQHRAKIEELRE HLLRWGFTTPDKKHQKEPPFLWMGYELHPDRWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYHGQVDCSPGMW QLCTHLEGKIILVAVHVASG YMEAEVIPAETGQETAYFILKLAGRWPVKTIHTNGSNFTSTTVKAACWWAGIQQE FGIPYNPQSQGVVSMNNELKKIIGQVREQAEHLKTAVQMAVFIHNFKRRGGIGGYSAGERIVDIIATDIQTRLQK QIIKIQNFRVYYRDSRDPLWKGPAKLLWKGEGAVVIQDNSEIKVVPRRKVKIIKDYG KQMAGDDCVASRQDED SEQ ID NO: 713 SIV GAG/NEF Hybrid VKLIEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIRDIINEEAADWDLQHPQPAPQQ GQLREPSGSDIAGTTSSVDEQIQWMYRQQNPIPVGNIYRRWIQLGLQKCVRMYNPTNILDVKQGPKEPFQSYVDR FYKSLRAEQTDAAVKNWMTQTLLIQNANPDCKLVLKGLGVNP TLEEMLTACQGVGGPGQKARLMAEALKDALTPG PIPFAAVQQRGQRKIIKCWNCGKTGHSARQCKAPRRKGCWKCGKAGHVMAKCPERQAGFLGFGPWGKKPHNFPMA QMPQGLTPTAPPADPAVDMLKNYMKMGKRQREKQRENRERPYKEVSEDLLHLSSLFGEDQPGGATSKRRSKPSGD LRQKLLRARGENYGRLWGELED GSSQSLGGLGKGLSSRSCEGQKYSQGQFMNTPWKNPAEEKEKLPYRKQNIDDV DEEDNDLVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGI RYPKTFGWLWKLVPVDMSNEAQEDDTHYLVHPAQTHQWSDPWGEVLVWKFDPLLAHTYEAFVRHPEE FGWKSGLP KEEVERRLAARGLLKMADKKETR SEQ ID NO: 714 gag/nef conserved from SIV MPVQQIGGNYVHLPLSPRTLNAWVKLIEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIRDIINE EAADWDLQHPQPAPQQGQLREPSGSDIAGTTSSVDEQIQWMYRQQNPIPVGNIYRR WIQLGLQKCVRMYNPTNIL DVKQGPKEPFQSYVDRFYKSLRAEQTDAAVKNWMTQTLLIQNANPDCKLVLKGLGVNPTLEEMLTACQGVGGPGQ KARLMVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARHRILDIYLEKEEGIIPDWQDYTSGPGIRY PKTFGWLWKLVP SEQ ID NO : 715 SIV pol hybrid MFFRAWPMGKEASQFPHGPDASGADTNCSPRGSSCGSTEELHEVGQKAERKAEGEQRETLQGGNGGFAAPQFSLW RRPVVTAHIEGQPVEVLLADDSIVTGIELGPHYTPKIVGGIGGFINTKEYKNVEIEVLGKRIKGTIMTGDTPINI FGRNLLTALGMSLNFPIAKVEPVKVALKPGKD GPKLKQWPLSKEKIVALREICEKMEKDGQLEEEAPPTNPYNTPT FAIKKKDKNKWRMLIDFRELNRVTQDFTEVQLGIPHPAGLAKRKRITVLDIGDAYFSIPLDEEFRQYTAFTLPSV NNAEPGKRYIYKVLPQGWKGSPAIFQYTMRHVLEPFRKANPDVTLVQILIASDRTDLEHDRVVLQSKELLNSIGF STPEEKFQ KDPPFQWMGYELWPTKWKLQKIELPQRETWTVNDIQKLVGVLNWAAQIYPGIKTKNLCKMIRGKMAL TEGVQWTELAEAELEENRIILNQEQEGRYYREDKPLEATVLKNQDNQWTYKIHQGDRILKVGKYAKVKNTHTNGI RLLANVVQKIGKESIVIWGQTPFFHLPVEREVWDQW WTDYWQATWIPDWDFVSTPPLIRLVFNLVKEPIEKEEVY YIDGSCNRNSKEGKAGYVTRDRGKEKVLVLEQATNQQALQAFLLALKDSGPKANIVTDSQYVLGIITGQPTESDSR IVAQIIEQMIKKSEVYIGWVPAHKGLGGNQEVDRLVSQEIRQVLFLESIEPAQEDHDKYHSNIKELAFKFGLPRL VAK QIVDTCNKCQQKGEAIHGQANSDLGTWQMCTHLEGKIIIVAVHVASGFIEAEVIPQETGRQTALFLLKLAGR WPITHLHTNGANFASQEVKMVAWWAGIEHTFGVPYNPQSQGVVAMNHHLKNQIDRIREQANSVETIVLMAVHCMN FKRRGGIGDMTPAERLINMITTEQEIQFQQSKNSKFKNFRVYYREGRDQ LWKGPGELLWKGEGAVILKVGTDIKV VPRRKAKIIKDYGGGKEVDSSSHMEDTGEAREVA SEQ ID NO: 716 pol conserved from SIV MPQFSLWRRPVVTAHIEGQPVEVLLADDSIVTGIELGPHYTPKIVGGIGGFINTKEYKNVEIEVLGKRIKGTIMT GDTPINIFGRNLLTALGMSLNFPIAKVEPVKVALKPGKDGPKLKQ WPLSKEKIVALREICEKMEKDGQLEEAPPT NPYNTPTFAIKKKDKNKWRMLIDFRELNRVTQDFTEVQLGIPHPAGLAKRKRITVLDIGDAYFSIPLDEEFRQYT AFTLPSVNNAEPGKRYIYKVLPQGWKGSPAIFQYTMRHVLEPFRKANPDVTLVQILIASDRTDLEHDRVVLQSKE LLNSIGFSTPEEKFQKDPPFQ WMGYELWPTKWKLQKIELD TEQEIQFQQ SKNSKFKNFRVYYREGRDQLWKGPGELLWKGEGAVILKVGTDIKVVPRRKAKIIKDYGGGKEVDSSSHMEDTGEA REVA SEQ ID NO: 717 HIV Pol Epigraph 1 B FFRENLAFPQGKAREFSSEQTRANSPTRRELQVWGRDNNSLSEAGADRQGTVSFSFPQITLWQRPLVTIKIGGQL KEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIG CTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS KIGPENPYNTPVFAIKKKDSTK WRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQ YNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKK HQKEPPFLWMGYELHPDKWTVQPIVL PEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVVPL TEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTE AVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKL WYQLEKEPIVGAETFYVDGA ANRETKLGKAGYVTDRGRQKVVSLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQ IIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKE IVASCDKCQLKGEAMHGQVDCSPGI WQLDCTHLEGKIILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPV KTIHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNF KRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRDPLWKGPAKLLWKGEGAV VIQDNSDIKVV PRRKAKIIRDYGKQMAGDDCVASRQDED SEQ ID NO: 718 HIV gag epigraph 1 SQNYPIVQNLQGQMVHQAISPR TLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAP GQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRF YKTLRAEQATQEVKNWMTETLLVQNANP DCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSAT IMMQRGNFKGQKRIKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQS RPEPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLKSLFGNDPLSQ SEQ ID NO: 719 Epigraph 1 conserved HIV M gag PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINE EAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSI LDIRQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNANPDCKTI LKALGPAATLEEMMTACQGVGGPG HKARVL SEQ ID NO: 720 HIV gag epigraph 2 NAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPP GQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIILGLNKIVRMYSPTSILDIKQGPKEPFRDYVDRF FKTLRAEQASQEVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGV GGPSHKARVLAEAMSQVTNSAT IMMQRGNFRNQRKTVKCFNCGKEGHLARNCRAPRKKGCWKCGREGHQMKDCNERQANFLGKIWPSNKGRPGNFPQ SRPEPTAPPAESFRFEETTPAPKQEPKDREPLTSLKSLFGSDPLSQ SEQ ID NO: 721 Conserved Epigraph 2 of HIV M gag PIVQNAQGQMVHQPLSPRTLNAWV KVIEEKAFSPEVIPMFTALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINE EAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIILGLNKIVRMYSPTSI LDIKQGPKEPFRDYVDRFFKTLRAEQASQEVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPS HK ARVL SEQ ID NO: 722 HIV M nef Epigraph 1 MGGKWSKSSIVGWPAVRERMRRAEPAAEGVGAVSRDLEKHGAITSSNTAATNADCAWLEAQEEEEVGFPVRPQVP LRPMTYKGALDLSHFLKEKGGLEGLIYSKKRQEILDLWVYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVDP REVEEANEGENNCLLHPMSQHGMDDPEKEVLMWKFDSRLAFHHMARELHPEYYKDC SEQ ID NO: 723 Epigraph 1 conserved nef of HIV M VGFPVRPQVPLRPMTYKGALDLSHFLKEKGGLEGL IYSKKRQEILDLWVYHTQGYFPDWQNYTPGPGIRYPLTFG WCFKLVP SEQ ID NO: 724 HIV M nef Epigraph 2 MGSKWSKSSIVGWPAIRERMRRTEPAAEGVGAASRDLERHGAITSSNTAANNADCAWLEAQEDEEVGFPVKPQVP LRPMTYKAAFDLSFFLKEKGGLDGLIYSQKRQDILDLWVYNTQG FFPDWQNYTPGPGVRYPLTFGWCFKLVPVEP EKVEEANEGENNSLLHPMSLHGMDDPEREVLMWKFDSSLARRHMARELHPEFYKDC SEQ ID NO: 725 Epigraph 2 conserved nef of HIV M VGFPVKPQVPLRPMTYKAAFDLSFFLKEKGGLDGLIYSQKRQDILDLWVYNTQGFFPDWQNYTPGPGVRYPLTFG WCFKL VP SEQ ID NO :726 HIV Pol Epigraph 1 M FFRENLAFPQGEAREFSSEQTRANSPTRRELQVWGRDNNSLSEAGADRQGTVSFSFPQITLWQRPLVTIKIGGQL KEALLDTGADDTVLEDINLPGKWKPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLVGPTPVNIIGRNLLTQIG CTLNFPISPIETVPVKLKPGMDGPKVKQWP LTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTK WRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQ YNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLKWGFTTPDKK HQKEPPFL WMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVKQLCKLLRGAKALTDIVPL TEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQDQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTE AVQKIATESIVIWGKTPKFRLPIQKETWETWWTEYWQAT WIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGA ANRETKLGKAGYVTDRGRQKVVSLTETTNQKTELQAIHLALQDSGSEVNIVTDSQYALGIIQAQPDKSESELVNQ IIEQLIKKEKVYLSWVPAHKGIGGNEQVDKLVSSGIRKVLFLDGIDKAQEEHEKYHSNWRAMASDFNLPPIVAKE IVASCDKC QLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPV KVIHTDNGSNFTSAAVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNF KRKGGIGGYSAGERIIDIIATDIQTKELQKQITKIQNFRVYYRDSRDPIW KGPAKLLWKGEGAVVIQDNSDIKVV PRRKAKIIRDYGKQMAGDDCVAGRQDEDQ SEQ ID NO: 727 Epigraph 1 conserved HIV pol M PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEDINLPGKWKPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV LVGPTPVNIIGRNLLTQIGCTLNFPISPIETV PVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG PENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRK YTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTK IEELRQ HLLKWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYHGQVD CSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKVIHTDNGSNFTSAAVKAAC WWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLK TAVQMAVFIHNFKRKGGIGGYSAGERIIDIIA TDIQTKELQKQITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDC VAGRQDEDQ SEQ ID NO: 728 HIV Pol Epigraph 2 M FFREDLAFPQGKAREFPSEQTRANSPTRGELQVWGGDNNSPSEAGADRQGTVSFSFPQITLWQRPLVSIKVGGQI KEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLIGPTPVNIIGRNMLTQLG CTLNFPISPIDTVPVTLKPGMDGPRVKQWPLTEEKIK ALTEICKEMEKEGKITKIGPENPYNTPIFAIKKKDSTK WRKLVDFRELNKKTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTIPSTTNNETPGIRYQ YNVLPQGWKGSPAIFQCSMTKILEPFRIKNPEIVIYQYMDDLYVGSDLEIGQHRAKIEELREHLLRWGFTTPDKK HQKEPPFLWMGY ELHPDRWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYAGIKVRQLCKLLRGTKALTEVVPL TEEAELELAENREILKTPVHGVYYDPSKDLVAEIQKQGQGQWTYQIYQEPYKNLKTGKYARKRSAHTNDVRQLTE VVQKIATESIVIWGKTPKFKLPIQKETWEAWWTDYWQATWIPD WEFVNTPPLVKLWYQLEKDPIVGAETFYVDGA ASRETKLGKAGYVTNRGRQKVVSLTDTTNQKTELHAIHLALQDSGLEVNIVTDSQYALGIIQAQPDRSESEVVNQ IIEELIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGIDKAQEEHERYHSNWRTMASDFNLPPVVAKE IVANCDKCQLKGE AIHGQVDCSPGMWQLDCTHLEGKIILVAVHVASGYMEAEVIPAETGQETAYFILKLAGRWPV LLWKGEGAVVIQDNSEIKVV PRRKVKIIKDYGKQMAGDDCVASRQDED SEQ ID NO: 729 Epigraph 2 conserved HIV pol M PQITLWQRPLVSIKVGGQIKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTV LIGPTPVNIIGRNMLTQLGCTLNFPISPIDTVPVTLKPGMDG PRVKQWPLTEEKIKALTEICKEMEKEGKITKIG PENPYNTPIFAIKKKDSTKWRKLVDFRELNKKTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDESFRK YTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRIKNPEIVIYQYMDDLYVGSDLEIGQHRAK IEELREHLLRWGF TTPDKKHQKEPPFLWMGYELHPDRWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYHGQVD CSPGMWQLDCTHLEGKIILVAVHVASGYMEAEVIPAETGQETAYFILKLAGRWPVKTIHTDNGSNFTSTTVKAAC WWAGIQQEFGIPYNPQSQGVVESMNNELKKIIGQVREQAEHLKTAVQMAVFI HNFKRRGGIGGYSAGERIVDIIA TDIQTRELQKQIIKIQNFRVYYRDSRDPLWKGPAKLLWKGEGAVVIQDNSEIKVVPRRKVKIIKDYGKQMAGDDC VASRQDED SEQ ID NO: 730 Epigraph 1 HIV B gag MGARASVLSGGELDRWEKIRLRPGGKKKYRLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEEL KSLYNTVATLYCVHQRIEVKDTKEALDKIEEEQNKSKKKAQQAAADTGNSSQVSQNYPIVQNLQGQMVHQAISPR TLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTML NTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAP GQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRF YKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSAT IMMQRGNFRNQRKTVKCF NCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQ SRPEPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLKSLFGNDPSSQ SEQ ID NO: 731 Conserved Epigraph 1 of HIV B gag PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQ AAMQMLKETINE EAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSI LDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPG HKARVL SEQ ID NO: 732 Epigraph 2 of HIV B MGAR gag ASVLSGGKLDKWEKIRLRPGGKKKYKLKHIVWASRELERFALNPGLLETSEGCKQILGQLQPALQTGSEEL RSLYNTVAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKRAQQAAADTGNNSQVSQNYPIVQNMQGQMVHQPISPR TLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQ ILKETINEEAADWDRLHPVHAGPVAP GQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRF YKVLRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPSHKARILAEAMSQVTNSAT IMMQKGNFRNQRKIVKCFNCGKEGHIARN CRAPRKKGCWKCGREGHQMKDCNERQANFLGKIWPSYKGRPGNFLQ NRPEPTAPPAESFRFGEETTTPPQKQEPIDKDLYPLASLRSLFGNDPSS SEQ ID NO: 733 Epigraph 2 conserved HIV B gag PIVQNMQGQMVHQPISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQILKETINE EAADWDRLHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRMYSPVSI LDIKQGPKEPFRDYVDRFYKV LRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPS HKARIL SEQ ID NO: 734 HIV B nef Epigraph 1 MGGKWSKSSIVGWPAVRERMRRAEPAAEGVGAVSRDLEKHGAITSSNTAATNADCAWLEAQEEEEVGFPVRPQVP LRPMTYKGALDLSHFLKEKGGLEGLIYSQKRQ DILDLWVYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVEP EKVEEANEGENNSLLHPMSQHGMDDPEKEVLMWKFDSRLAFHHMARELHPEYYKDC SEQ ID NO: 735 HIV B nef conserved Epigraph 1 GFPVRPQVPLRPMTYKGALDLSHFLKEKGGLEGLIYSQKRQDILDLWVYHTQGYFPDWQNY TPGPGIRYPLTFGW CFKLVP SEQ ID NO: 736 HIV B nef epigraph 2 MGGKWSKSSVVGWPAIRERMRRAEPAADGVGAASRDLERHGAITSSNTAANNAACAWLEAQEDEEVGFPVKPQVP LRPMTYKAAVDLSHFLKEKGGLEGLIHSQKRQEILDLWVYHTQGFFPDWQNYTPGPGTRFPLTFGWCFKLVPVDP DKVEEANEGENNCLLHPMSLHGMDDPEREVLVWKFDSRLA FHHVARELHPEYYKNC SEQ ID NO: 737 Epigraph 2 Conserved from HIV B nef GFPVKPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQKRQEILDLWVYHTQGFFPDWQNYTPGPGTRFPLTFGW CFKLVP SEQ ID NO: 738 Epigraph 1 from HIV B pol FFRENLAFPQGKAREFSSEQTRANSPTRRELQVWGRDN NSLSEAGADRQGTVSFSFPQITLWQRPLVTIKIGGQL KEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIG CTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTK WRKLVDFRELNKRTQDF WEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQ YNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKK HQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVK QLCKLLRGTKALTEVVPL TEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTE AVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGA ANRETKLGKAGYVTDRGRQ KVVSLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQ IIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKE IVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKIILVAVHVASGYIEAEVIPAETGQET AYFLLKLAGRWPV KTIHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNF KRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRDPLWKGPAKLLWKGEGAVVIQDNSDIKVV PRRKAKIIRDYGKQMAGDDCVASRQDED SEQ ID NO: 739 Epigraph 1 Conserved from HIV B pol PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTV LVGPTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTE MEKEGKISKIG PENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRK YTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTK IEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDK WTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYHGQVD CSPGIWQLDCTHLEGKIILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSTTVKAAC WWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIA KEALL DTGADDTVLEDMNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLIGPTPVNIIGRNLLTQLG CTLNFPISPIDTVPVKLKPGMDGPRVKQWPLTEEKIKALIEICTEMEKEGKISRIGPENPYNTPIFAIKKKDSTK WRKLVDFRELNKKTQDFWEVQLGIPHPSGLKKKKSVTVLDVGDAYFSVPLDKEFRKYTAFT IPSTNNETPGIRYQ YNVLPQGWKGSPAIFQCSMTKILEPFRKQNPEIVIYQYMDDLYVGSDLEIEQHRTKIEELRQHLLKWGFTTPDKK HQKEPPFLWMGYELHPDKWTVQPIMLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGAKALTEVIPL TEEAELELAENREILREILREPVHGVYYDPTKDL IAEIQKQGLGQWTYQIYQEPYKNLKTGKYARTRGAHTNDVRQLTE AVQKITTESIVIWGKTPKFRLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGA ANRDTKLGKAGYVTNKGRQKVVTLTDTTNQKTELQAIYLALQDSGSEVNIVTDSQYALGIIQA QPDKSESELVNQ IIEQLIKKEKIYLAWVPAHKGIGGNEQVDKLVSSGIRKVLFLDGIDKAQEDHEKYHSNWKAMASDFNLPPIVAKE IVASCDKCQLKGEAIHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFILKLAGRWPV KTVHTDNGSNFTSATVKAACWWAGVKQEFGIPYNPQ SQGVVESMNNELKKIIGQIRDQAEHLKTAVQMAVFIHNF KRKGGIGGYSAGERIIDIIATDIQTRELQKQITKIQNFRVYYRDNRDPLWKGPAKLLWKGEGAVVIQDNSEIKVV PRRKVKIIRDYGKQMAGDDCVAGRQDED SEQ ID NO: 741 Epigraph 2 Conserved from HIV B pol PQITLWQRPLVTIKVGGQLKEALLDTGADDTVLEDMNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTV LIGPTPVNIIGRNLLTQLGCTLNFPISPIDTVPVKLKPGMDGPRVKQWPLTEEKIKALIEICTEMEKEGKISRIG PENPYNTPIFAIKKKDSTKWRK LVDFRELNKKTQDFWEVQLGIPHPSGLKKKKSVTVLDVGDAYFSVPLDKEFRK YTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQCSMTKILEPFRKQNPEIVIYQYMDDLYVGSDLEIEQHRTK IEELRQHLLKWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIMLPEKDSWTVNDIQKLVGKLN WASQIYHGQVD CSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFILKLAGRWPVKTVHTDNGSNFTSATVKAAC WWAGVKQEFGIPYNPQSQGVVESMNNELKKIIGQIRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIIDIIA TDIQTRELQKQITKIQNFRVYYRDNRDPL WKGPAKLLWKGEGAVVIQDNSEIKVVPRRKVKIIRDYGKQMAGDDC VAGRQDED SEQ ID NO: 742 HIV gag epigraph 1 QKTQQAKAADGKVSQNYPIVQNLQGQMVHQAISPRTLN AWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIAPGQM REPRGSDIAGTTSTLQEQIAWMTSNPPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKT LRAEQ ATQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQANSNIMMQR SNFKGPKRIVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRPEP TAPPAEPTAPPAESFRFEETTPAPKQEPKDREPLTSLKSLFGSDPLSQ SEQ ID NO: 74 3 Epigraph 1 Preserved from gag of HIV C PIVQNLQGQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINE EAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIAWMTSNPPIPVGDIYKRWIILGLNKIVRMYSPVSI LDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANP DCKTILRALGPGATLEEMMTACQGVGGPG HKARVL SEQ ID NO: 744 HIV C gag Epigraph 2 MGARASVLRGEKLDKWERIRLRPGGKKRYMLKHIVWASRELEKFALNPGLLETAEGCKQIIKQLHPALQTGTEEL KSLFNTVATLYCVHKKIDVRDTKEALDKIEEEQNKCQQKTQQAEAADKGKVSQ NYPIVQNLQGQMVHQALSPRTL NAWVKVVEEKAFSPEIIPMFTALSEGATPTDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPVAPGQ MREPRGSDIAGTTSNLQEQIAWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFK VLRAEQATQEVKNWMTETLLVQNANP DCKTILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMSQANNANIMM QRSNFKGSKRIVKCFNCGKEGHIAKNCRAPRKKGCWKCGREGHQMKDCNERQANFLGKIWPSNKGRPGNFLQNRP EPTAPPAEPTAPPAESFKFEETTPAPKQESKDREPLISLKSLFGNDPLSQ SEQ ID NO: 745 Epigraph 2 Preserved HIV gag B NPDCKTILRALGPGASLEEMMTACQGVGGPS HKARVL SEQ ID NO: 746 Epigraph 1 de nef de HIV C MGGKWSKSSIVGWPAVRERIRRTEPAAEGVGAASQDLDKYGALTSSNTAHNNADCAWLQAQEEEEEVGFPVRPQV PLRPMTYKAAFDLSFFLKEKGGLEGLIYSKKRQEILDLWVYHTQGFFPDWQNYTPGPGVRYPLTFGWCFKLVPVD PREVEEANEGENNCLLHPMSQHGMEDEDREVLKWQFDSSLARRHMARELHPEYYKDC SEQ ID NO: 747 Epigraph 1 Conservado de nef de HIV C GFPVRPQVPLRPMTYKAAFDLSFFLKEKGGLEGLIYSKKRQEILDLWVYHTQGFFPDWQNYTPGPGVRYPLTFGW CFKLV SEQ ID NO: 748 Epigraph 2 de nef de HIV C MGSKWSKSSIVGWPAVRERMRRAEPAAEGVGAASRDLDKHGALTSSNTPANNADCAWLEAQEEEGEVGFPVKPQV PLRPMTYKGAFDLGFFLKEKGGLDGLIYSKKRQDILDLWVYNTQGYFPDWQNYTPGPGIRYPLTFGWCYKLVPVD PSEVEEANKGENNCLLHPMSLHGMEDEHREVLKWKFDSSLARRHLAREKHPEFYKDC SEQ ID NO: 749 Epigraph 2 Conservado de nef de HIV C GFPVKPQVPLRPMTYKGAFDLGFFLKEKGGLDGLIYSKKRQDILDLWVYNTQGYFPDWQNYTPGPGIRYPLTFGW CYKLV SEQ ID NO: 750 HIV Pol Epigraph 1 C FFRENLAFPQGEAREFPSEQTRANSPTSRANSPTSRELQVRGDNPRSEAGAERQGTLNFPQITLWQRPLVSIKVG GQIKEALLDTGA DDTVLEEINLPGKWKPKMIGGIGGFIKVRQYDQILIEICGKKAIGTVLVGPTPVNIIGRNMLT QLGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALTAICEEMEKEGKITKIGPENPYNTPVFAIKKKD STKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEGFRKYTAFT IPSINNETPGI RYQYNVLPQGWKGSPAIFQSSMTKILEPFRAQNPEIVIYQYMDDLYVGSDLEIGQHRAKIEELREHLLKWGFTTP DKKHQKEPPFLWMGYELHPDKWTVQPIQLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGAKALTDI VPLTEEAELELAENREILKEPVHGVYYD PSKDLIAEIQKQGHDQWTYQIYQEPFKNLKTGKYAKMRTAHTNDVKQ LTEAVQKIAMESIVIWGKTPKFRLPIQKETWETWWTDYWQATWIPEWEFVNTPPLVKLWYQLEKEPIAGAETFYV DGAANRETKIGKAGYVTDRGRQKIVSLTETTNQKTELQAIQLALQDSGSEVNIVTDSQYAL GIIQAQPDKSESEL VNQIIEQLIKKERVYLSWVPAHKGIGGNEQVDKLVSSGIRKVLFLDGIDKAQEEHEKYHSNWRAMASEFNLPPIV AKEIVASCDKCQLKGEAIHGQVDCSPGIWQLDCTHLEGKIILVAVHVASGYIEAEVIPAETGQETAYYILKLAGR WPVKVIHTDNGSNFTSAAVKAACWWAGIQQEFG IPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFI HNFKRKGGIGGGYSAGERIIDIIATDIQTKELQKQIIKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDI KVVPRRKVKIIKDYGKQMAGADCVAGRQDEDQ SEQ ID NO: 751 Epigraph 1 Preserved from HIV C pol PQIT LWQRPLVSIKVGGQIKEALLDTGADDTVLEEINLPGKWKPKMIGGIGGFIKVRQYDQILIEICGKKAIGTV LVGPTPVNIIGRNMLTQLGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALTICEEMEKEGKITKIG PENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKK SVTVLDVGDAYFSVPLDEGFRK YTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRAQNPEIVIYQYMDDLYVGSDLEIGQHRAK IEELREHLLKWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIQLPEKDSWTVNDIQKLVGKLNWASQIYHGQVD CSPGIWQLDCTHLEGKI ILVAVHVASGYIEAEVIPAETGQETAYYILKLAGRWPVKVIHTDNGSNFTSAAVKAAC WWAGIQQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIIDIIA TDIQTKELQKQIIKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDIK VVPRRKVKIIKDYGKQMAGADC VAGRQDEDQ SEQ ID NO: 752 HIV C Pol Epigraph 2 FFRENLAFQQGEAREFPSEQARANSPTSRANSPTSRELQVRGDNPCSEAGAERQGTFNFPQITLWQRPLVTIKVG GQIKEALLDTGADDTVLEDINLPGKWKPRMIGGIGGFIKVRQYDQIPIEICGKKAIGSVLVGPTPVNIIGRNLLT QLGCTLNFPISPIETI PVKLKPGMDGPRVKQWPLTEEKIKALTEICEEMEKEGKISKIGPENPYNTPIFAIKKKD STKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTIPSTTNNETPGI RYQYNVLPQGWKGSPAIFQSSMTRILEPFRAKNPEIVIYQYMDDLYVGSDLEIEQHRAKIEELRE HLLRWGFTTP DKKHQKEPPFLWMGYELHPDKWTVQPIQLPEPKESWTVNDIQKLVGKLNWASQIYPGIKVKQLCKLLRGTKALTDI VPLTEEAELELAENREILREPVHGVYYDPSKELIAEIQKQGQDQWTYQIYQEPFKNLKTGKYAKRRTAHTNDVRQ LTEAVQKIALESIVIWGKIPKFR LPIQKETWEIWWTDYWQATWIPDWEFVNTPPLVKLWYQLEKEPIAGVETFYV DGAANRETKLGKAGYVTDKGRQKIVTLTETTNQKAELQAIQLALQDSGPEVNIVTDSQYALGIIQAQPDKSESEI VNQIIEQLINKERIYLSWVPAHKGIGGNEQVDKLVSNGIRKVLFLDGIDKAQEEHEKYHNNW RAMASDFNLPPVV AKEIVASCDQCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYMEAEVIPAETGQETAYFILKLAGR WPVKIIHTDNGSNFTSTAVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVREQAEHLKTAVQMAVFI HNFKRRGGIGGYSAGERIIDIIASDIQTKELQKQ ITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVLQDNSDI KVVPRRKAKIIRDYGKQMAGDDCVAGRQDED SEQ ID NO: 753 Epigraph 2 Conserved from HIV C pol PQITLWQRPLVTIKVGGQIKEALLDTGADDTVLEDINLPGKWKPRMIGGIGGFIKVRQYDQIPIEICGKKAIGSV LVGPTPVNIIGRN LLTQLGCTTLNFPISPIETIPVKLKPGMDGPRVKQWPLTEEKIKALTEICEEMEKEGKISKIG PENPYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDESFRK YTAFTIPSTTNNETPGIRYQYNVLPQGWKGSPAIFQSSMTRILEPFRAKNPEIVIYQYMDDLYV GSDLEIEQHRAK IEELREHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIQLPEPKESWTVNDIQKLVGKLNWASQIYHGQVD CSPGIWQLDCTHLEGKVILVAVHVASGYMEAEVIPAETGQETAYFILKLAGRWPVKIIHTDNGSNFTSTAVKAAC WWAGIKQEFGIPYNPQSQGVVESMNKEL KKIIGQVREQAEHLKTAVQMAVFIHNFKRRGGIGGYSAGERIIDIIA SDIQTKELQKQITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVLQDNSDIKVVPRRKAKIIRDYGKQMAGDDC VAGRQDE SEQ ID NO: 754 EG-0 HIV M Gag episense, Custom MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELERFALNPGLLETSEGCRQILGQLQPSLQTGSEEL KSLYNTVATLYCVHQRIEVKDTKEALDKIEEEQNKSKKKAQQAAADTGNSSQVSQNYPIVQNLQGQMVHQAISPR TLNAWV KVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAP GQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRF YKTLRAEQATQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARV LAEAMSQVTNSAT IMMQRGNFKGQKRIKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQS RPEPTAQSRPEPTAPPAESFRPQPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLKSLFGNDPLSQY SEQ ID NO: 755 EG-0 Conserved HIV M gag episense, Custom P IVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINE EAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSI LDIRQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNANPDCKTILK ALGPAATLEEMMTACQGVGGPG HKARVL SEQ ID NO: 756 CEN-1 HIV gag M, Custom MGARASVLTGGKLDAWERIRLRPGGKKKYRMKHLVWASRELERFAINPGLLETAEGCQQIIEQLQSTLKTGSEEL KSLFNTVATLWCVHQRIEIKDTKEALDKLEEVQNKSQQKTQQAAAGTGSSSKVSQNYPIVQNAQGQMVHQPLSPR TLNAWVKVVEEKGFNPEVIPM FSALSDGATPQDLNMMLNIVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPP GQMREPRESDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIILGLHKIVRMYSPVGILDIKQGPKEPFRDYVDRF FKTLRAEQASQEVKNWMTETLLIQNANPDCKSILKALGTGATLEEMMTACQGVGGPSHKARVLAEAMSQA QHANI MMQRGNFKGQRKIKCFNCGKEGHLARNCRAPRKRGCWKCGQEGHQMKDCNERQANFLGKIWPSNKGRPGNFPQSR PEPTAPRTEPTAPPARPEPTAPPLQSRLEPTAPPAEPTAPPAENWGMGEEITSLLKQEQKDKEHPPPLVSLKSLF GNDPLLQ SEQ ID NO: 757 CEN-1 Preserved HIV M gag, Custom P IVQNAQGQMVHQPLSPRTLNAWVKVVEEKGFNPEVIPMFSALSDGATPQDLNMMLNIVGGHQAAMQMLKDTINE EAAEWDRVHPVHAGPIPPGQMREPRESDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIILGLHKIVRMYSPVGI LDIKQGPKEPFRDYVDRFFKTLRAEQASQEVKNWMTETLLIQNANP DCKSILKALGTGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 758 HIV M gag CEN-2, Custom MGARASILRGGKLDKWEKIRLRPGGKKHYMLKHIVWASRELEKFALNPDLLETSEGCKQIIKQLQPALQTGTEEL RSLFNTVATLYCVHEKIEVRDTKEALDKVEEEQNKSQQKTQQAKAADGKVSQNYPIVQNAQGQMVHQALSPRTLN AWVKVIEEKAFSPEVIPMFTALSEGATPSDLNTMLNTIGGHQ AAMQMLKDTINEEAAEWDRVHPVHAGPVAPGQM REPRGSDIAGSTSTLQEQIAWMTSNPPIPVGDIYKRWIILGLNKIVKMYSPVSILDIKQGPKEPFRDYVDRFFKT LRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQANSNIMMQR SNFKGPKRIVKCFNC GKEGHIAKNCRAPRKKGCWKCGREGHQMKDCNERQANFLGKIWPSNKGRPGNFLQNRPEP TAPPLQSRLEPTAPLEPTAPPEPTAPPAVVPTAPPVEPTAPPAEPTAPPAESFRFEETTPAPKQEPKDREPLTSL KSLFGSDPLSQ SEQ ID NO: 759 CEN-2 Conserved from HIV M gag, Custom PIVQNAQGQMVHQALSPRTL NAWVKVIEEKAFSPEVIPMFTALSEGATPSDLNTMLNTIGGHQAAMQMLKDTINE EAAEWDRVHPVHAGPVAPGQMREPRGSDIAGSTSTLQEQIAWMTSNPPIPVGDIYKRWIILGLNKIVKMYSPVSI LDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 760 HIV M gag CEN-3, Custom MGSRASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCKQILGQLQPALQTGSEEL RSLYNTVAVLYCVHQRIDVKDTKEALEKIEEEQNKCKKKAQQAAAAADTGNNSQVSQNYPIVQNIQGQMVHQALS PRTLNA WVKVIEEKAFSPEVIPMFTALSEGATPSDLNTMLNTIGGHQAAMQMLKDTINEEAADWDRLHPVQAGPV APGQMRDPRGSDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIIMGLNKIVRMYSPTSILDIKQGPKEPFRDYVD RFFKTLRAEQASQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPSHKAR VLAEAMSQATNS AAIMMQRGNFRNQRKIVKCFNCGKEGHIAKNCRAPRKRGCWKCGREGHQMKDCNERQANFLGRIWPSNKGRPGNF LQNRPEPTAPNFLQSRPEPSAPPEPTAPPEESFRFGEETATPSQKQEPTDKELYPLASLRSLFGNDPSSQ SEQ ID NO: 761 CEN-3 Preserved HIV M gag, Custom PIVQNIQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPSDLNTMLNTIGGHQAAMQMLKDTINE EAADWDRLHPVQAGPVAPGQMRDPRGSDIAGTTSNLQEQIGWMTSNPPIPVGDIYKRWIIMGLNKIVRMYSPTSI LDIKQGPKEPFRDY VDRFFKTLRAEQASQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 762 HIV M gag CEN-4, Custom MGTRASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETAEGCRQILEQLQPALQTGSEEL RSLYNTVAVLYCVHQRIDVKDT KEALEKIEEEQNKCKKKAQQTAADTGNNSQVSQNYPIVQNMQGQMVHQPISPR TLNAWVKVIEEKAFSPEVIPMFTALSEGATPHDLNTMLNTIGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPVAP GQMREPKGSDIAGTTSNLQEQIGWMTHNPPIPVGDIYKRWIIMGLNKIVRMYSPTSILDIKQGPK EPFRDYVDRF FKTLRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMSACQGVGGPSHKARILAEAMSQATNSAN IMMQRGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKRGCWKCGREGHQMKDCNERQANFLGKIWPSYKGRPGNFLQ NRPEPTAPPEPTAPPEESFGFGEETTTPPQKQEPIDKDLYPLASLRSL FGNDPSSQ SEQ ID NO: 763 CEN-4 Conserved from HIV gag M, Custom PIVQNMQGQMVHQPISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPPHDLNTMLNTIGGHQAAMQMLKDTINE EAAEWDRVHPVHAGPVAPGQMREPKGSDIAGTTSNLQEQIGWMTHNPPIPVGDIYKRWIIMGLNKIVRMYSPTSI LDIKQGPKEPFRDYVDRFFKTLRAEQASQ DVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMSACQGVGGPS HKARIL SEQ ID NO: 764 HIV M gag CEN-5, Custom MGARASILSGGKLDAWERIRLRPGGKKKYRMKHLVWASRELDRFALNPSLLETAEGCQQIMEQLQPALKTGTEEL RSLFNTVATLYCVHQRIDVKDTKEALDKIEEIQNKSK QKTQQAAADTGNSSKVSQNYPIVQNAQGQMIHQSLSPR TLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPP GQMREPRGGDIAGTTSTPQEQIGWMTSNPPIPVGDIYKRWIILGLHKLVRMYSPVSILDIKQGPKEPFRDYVDRF FKTLRA EQATQEVKGWMTETLLIQNANPDCKSILRALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQVQHTNI MMQRGNFRGQKRIKCFNCGKEGHLARNCRAPRKRGCWKCGREGHQMKDCNERQANFLGKIWPSSKGRPGNFPQSR PEPTAPQNRLEPTAPPAEPTAPPAEIFGMGEEITSPPKQEQKDREQAPPLVSLK SLFGNDLLSQ SEQ ID NO: 765 CEN-5 Preserved HIV M gag, Custom PIVQNAQGQMIHQSLSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINE EAAEWDRVHPVHAGPIPPGQMREPRGGDIAGTTSTPQEQIGWMTSNPPIPVGDIYKRWIILGLHKLVRMYSPVSI LDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLIQNANP DCKSILRALGPGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 766 EG-0 HIV C gag episense, Custom MGARASILRGGKLDKWEKIRLRPGGKKHYMLKHLVWASRELERFALNPGLLETSEGCKQIMKQLQPALQTGTEEL RSLYNTVATLYCVHEKIEVRDTKEALDKIEEEQNKSQQKTQQAKAADG LRAEQATQDVKNWMTDTL LVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQANSNIMMQR SNFKGPKRIVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRPEP TAPPAEPTAPPAESFRFEETTPAPKQEPKDREPLTSLKSLFGSDPLSQ SEQ ID NO: 767 EG-0 episense Preserved from HIV C gag, Custom PIVQNLQGQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINE EAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLQEQIAWMTSNPPIPVGDIYKRWIILGLNKIVRMYSPVSI LDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWM TDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPG HKARVL SEQ ID NO: 768 CEN-1 HIV C gag, Custom MGARASILRGEKLDKWEKIKLRPGGKKRYMLKHLIWASRELERFALNPSLLETSEGCKQIIKQLQPALKTGTEEL RSLFNTVATLYCVHAGIEVRDTKEALDRIEEEQNKCQQKTQQAEAADKGKVSQNYPIVQNAQGQMVHQALSPRTL NAWVKVVEEKAFSPEI IPMFTALSEGATPSDLNSMLNTVGGHQAAMQMLKDTINDEAAEWDRVHPVHAGPIAPGQ MREPRGSDIAGTTSNLQEQIAWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFK CLRAEQATQEVKNWMTDTLLIQNANPDCKTILKALGPGASLEEMMTACQGVGGPSHKARVLAEAMSQVNNA NIMM QRGNFKGPKRIIKCFNCGKEGHLARNCRAPRKKGCWKCGQEGHQMKDCSNERQANFLGKLWPSHKGGRPGNFLQN RPEPTAPPVEPTAPPAEPTAPPAESFKFEETTPVPKQELKDREPLISLKSLFGNDPLSQ SEQ ID NO: 769 CEN-1 Preserved HIV C gag, Customized IVQNAQGQMVHQALSPRTLNAWV KVVEEKAFSPEIIPMFTALSEGATPSDLNSMLNTVGGHQAAMQMLKDTINDE AAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSNLQEQIAWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSIL DIRQGPKEPFRDYVDRFFKCLRAEQATQEVKNWMTDTLLIQNANPDCKTILKALGPGASLEEMMTACQGVGGPSH K ARVL SEQ ID NO: 770 CEN-2 HIV C gag, Custom MGARASILRGEKLDKWERIRLRPGGKKHYMIKHLVWASRELEKFALNPGLLETADGCKQIIKQLHPALQTGTEEL KSLYNTVATLYCVHERIEVRDTKEALDRIEEEQNKCQQKTQQAEAADKGKVSQNYPIVQNAQGQMVHQPISPRTL NAWVKVVEEKAFSPEIIPMFTALSEGATPTDLNTMLNTIGGH QAAMQILKDTINEEAVEWDRLHPVQAGPVAPGQ IREPRGSDIAGTTSNLQEQIAWMTGNPPVPVGDIYKRWIIMGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFK VLRAEQATQEVKNWMTETLLVQNANPDCKIILKGLGPAATLEEMMTACQGVGGPSHKARVLAEAMSQVNNTNIMM QKSNFKGPKRTVKCFNC GKEGHIAKNCRAPRKKGCWKCGREGHQMKDCNERQANFLGKIWPSQKGRPGNFLQNRP EPTAPRPEPTAPPRLEPTAPPAEPSAPPAESFRFEGTTPAPKQESKDREPLISLKSLFGNDPLSQ SEQ ID NO: 771 CEN-2 Conserved HIV C gag, Custom PIVQNAQGQMVHQPISPRTLNAWVKVVEEKAFSPEIIPMF TALSEGATPTDLNTMLNTIGGHQAAMQILKDTINE EAVEWDRLHPVQAGPVAPGQIREPRGSDIAGTTSNLQEQIAWMTGNPPVPVGDIYKRWIIMGLNKIVRMYSPVSI LDIRQGPKEPFRDYVDRFFKVLRAEQATQEVKNWMTETLLVQNANPDCKIILKGLGPAATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 77 2 CEN-3 gag HIV C, Custom MGARASILRGEKLDRWERIRLRPGGKKCYMLKHIVWASRELERFSLNPGLLETAEGCKQIIKQLHPALQTGTEEL KSLFNTVATLYCVHKKIDVRDTKEALDKVEEEQNKCQQKTQQAKAADEKVSQNYPIVQNIQGQMVHQALSPRTLN AWVKVVEEKAFSPEIIPMFTAL SEEATPQDLNTMLNAVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQM REPRGSDIAGTTSNLQEQIAWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFRV LRAEQATQEVKNWMTDTLLIQNANPDCKTILKALGPGASLEEMMTACQGVGGPSHKARVLAEAMSQANNINIMMQ RGNFKGPKRTVKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCNERQANFLGRIWPSHKGRPGNFLQNRPE PTAPSAESFRQNRTEPTAPPARLEPTAPPAEPSAPPVESFRFEETTPALKQESKDREPLTSLRSLFGSDPLFQ SEQ ID NO: 773 CEN-3 Preserved HIV C gag, Custom PIVQNIQGQMVHQALSPRTLNAWVKVVEEKAFSPEIIPMFTALSEEATPQDLNTMLNAVGGHQAAMQMLKETINE EAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSNLQEQIAWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPVSI LDIRQGPKEPFR DYVDRFFRVLRAEQATQEVKNWMTDTLLIQNANPDCKTILKALGPGASLEEMMTACQGVGGPS HKARVL SEQ ID NO: 774 CEN-4 HIV C gag, Custom MGARASVLRGEKLDKWERIRLRPGGKKQYMLKHIVWASRELEKFALNPGLLETAEGCKQIIKQLHPALQTGTEEL RSLFNTVATLYCVHKGIDVR DTKEALDKVEEEQNKCQQKTQQAEADKKVSQNYPIVQNIQGQMVHQPLSPRTLNA WVKVVEEKAFSPEVIPMFSALSEGATPGDLNTMLNTIGGHQAAMQMLKDTINDEAAEWDRLHPVHAGPIAPGQMR EPRGSDIAGTTSNLQEQIAWMTNNPPVPVGEIYKRWIVLGLNKIVRMYSPVSILDIRQGPKEPFRDYVD RFFRTL RAEQATQEVKNWMTETLLVQNANPDCKNILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMSQANNTNIMMQK SNFKGPRRIVKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCNERQANFLGKIWPSNKGRPGNFLQNRPEP TAPQSRPEPTAPLEPTAPPAEPTAPPAESFKFEETTPAPKQEQKDR EPLISLKSLFGNDPLSQ SEQ ID NO: 775 CEN-4 Preserved from HIV C gag, Custom PIVQNIQGQMVHQPLSPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPGDLNTMLNTIGGHQAAMQMLKDTIND EAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSNLQEQIAWMTNNPPVPVGEIYKRWIVLGLNKIVRMYSPVSI LDIRQGPKEPFRDYVDRFFRTLRAEQATQEVKNWM TETLLVQNANPDCKNILRALGPGASLEEMMTACQGVGGPS HKARVL SEQ ID NO: 776 HIV C gag CEN-5, Custom MGARASVLRGEKLDKWERIRLRPGGKKRYMLKHIVWASRELEKFALNPGLLETAEGCKQIIKQLQPALQTGTEEL KSLFNTVATLYCVHEKIDVRDTKEALDRIEEEQNKCQQKTQQA KAADEKVSQNYPIVQNAQGQMVHQALSPRTLN AWVKVIEEKGFNPEVIPMFTALSDGATPQDLNSMLNTVGGHQAAMQILKDTINEEAAEWDRVHPVHAGPIAPGQM REPRGSDIAGTTSNLQEQIAWMTGNPPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKA LRAEQATQEVKN WMTETLLVQNANPDCKNILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMSQANNTNIMMQ RNNFKGPKRIIKCFNCGKEGHIAKNCRAPRKKGCWKCGREGHQMKDCNERQANFLGRIWPSHKGGRPGNFLQNRP EPTAPPVEPTAPPAEPTAPPAESFKFEETTPTPKQEQKDREPLISLKSLFGNDPLSQ SEQ ID NO: 77 7 CEN-5 Preserved HIV C gag, Custom PIVQNAQGQMVHQALSPRTLNAWVKVIEEKGFNPEVIPMFTALSDGATPQDLNSMLNTVGGHQAAMQILKDTINE EAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSNLQEQIAWMTGNPPIPVGEIYKRWIILGLNKIVRMYSPVSI LDIRQGPKEPFRDYVDRFFKALRA EQATQEVKNWMTETLLVQNANPDCKNILRALGPGASLEEMMTACQGVGGPS HKARVL SEQ ID NO: 778 EG-0 HIV B gag episense, Customized AISPR TLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAP GQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRF YKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQG VGGPGHKARVLAEAMSQVTNSAT IMMQRGNFRNQRKTVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQ SRPEPTAPPEPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLKSLFGNDPSSQ SEQ ID NO: 779 EG-0 Preserved HIV B gag episense, Custom PIVQNLQG QMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINE EAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSI LDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLE EMMTACQGVGGPG HKARVL SEQ ID NO: 780 HIV C gag CEN-1, Custom MGSRASVLSGGKLDQWEKIRLRPGGKKRYKLKHLVWASRELERFAVNPSLLETSEGCKQILGQLQPALQTGSEEL RSLYNTIAVLYCVHQRIEVKDTKEALEKIEEEQNKCKKKAQQAAAAAADTGNSNQVSQNYPIVQNMQGQMVHQAL SPRTLNAWVKVIEEKAFSPEVIPMF TALSEGATPADLNTMLNTIGGHQAAMQILKETINEEAAEWDRVHPVHAGP VAPGQMREPRGSDIAGSTSTLQEQIAWMTSNPPIPVGDIYKRWIIMGLNKIVRMYSPTSILDIKQGPKEPFRDYV DRFYKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQVTT PPAI MMQRGNFKNQRKIVKCFNCGKEGHLARNCRAPRKRGCWKCGREGHQMKDCSERQANFLGKIWPSYKGRPGN FLQNRPEPTAPPAEPTAPPAESFRFGEETATPPQKQEPIDKEMYPLTSLRSLFGNDPSQ SEQ ID NO: 781 CEN-1 Conserved from HIV B gag, Custom PIVQNMQGQMVHQALSPRTLNAWVKVIEE KAFSPEVIPMFTALSEGATPADLNTMLNTIGGHQAAMQILKETINE EAAEWDRVHPVHAGPVAPGQMREPRGSDIAGSTSTLQEQIAWMTSNPPIPVGDIYKRWIIMGLNKIVRMYSPTSI LDIKQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 782 HIV C gag CEN-2 , custom NTMLNTIGGHQAAMQILKETINDEAAEWDRTHPVHAGPV APGQMRDPRGSDIAGTTSNLQEQIGWMTHNPPIPVGDIYKRWIIMGLNKIVRMYSPVSILDIKQGPKEPFRDYVD RFYKILRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQMTNS ATIMMQKGNFRNQRK TIKCFNCGKEGHLARNCRAPRKRGCWKCGQEGHQMKDCNERQANFLGKIWPSSKGRPGNF LQSRPESRPEPTAPPAEPTAPPAESFRFGEETATPPQKQEPIDKEMYPLASLRSLFGNDPSSK SEQ ID NO: 783 CEN-2 Preserved HIV B gag, Custom PIVQNIQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMF TALSEGATPPHDLNTMLNTIGGHQAAMQILKETIND EAAEWDRTHPVHAGPVAPGQMRDPRGSDIAGTTSNLQEQIGWMTHNPPIPVGDIYKRWIIMGLNKIVRMYSPVSI LDIKQGPKEPFRDYVDRFYKILRAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 784 HIV C gag CEN-3, Customized EGATPGDLNLMLNAVGGHQAAMQMLKDTINEEAADWDRLHPVQAGP VAPGQLREPRGSDIAGTTSNLQEQIAWMTHNPPIPVGEIYKRWIIMGLNKIVRMYSPVSILDIKQGPKEPFRDYV DRFYRTLRAEQASQDVKNWMTETLLIQNANPDCRTILKALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQATS SATIMMQK GNFRNQRKIVKCFNCGKEGHIAKNCRAPRKRGCWKCGREGHQMKDCSERQANFLGKIWPSYKGRPGN FLQNRPEPTAPPAEPTAPPAESFRFGEETTTPPQKQEPTDKELYPLASLRSLFGNDPLSQ SEQ ID NO: 785 CEN-3 Conserved HIV B gag, Custom PIVQNIQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPGDLNLMLNAVGGHQAAMQMLKDTINE EAADWDRLHPVQAGPVAPGQLREPRGSDIA GTTSNLQEQIAWMTHNPPIPVGEIYKRWIIMGLNKIVRMYSPVSI LDIKQGPKEPFRDYVDRFYRTLRAEQASQDVKNWMTETLLIQNANPDCRTILKALGPGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 786 CEN-4 HIV C gag, Custom MGARASILSGGELDKWEKIRLRPGGKKKYRLKHIVWASNELERF ALNPGLLETSDGCRQILGQLHPSLQTGSEEL RSLYNTVAVLYCVHQRIEIKDTKEALEKIEEEQNKCKKKAQQAAAAQQAAAGTGNNSQVSQNYPIVQNMQGQMVH QALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPPHDLNTMLNTIGGHQAAMQILKETINEEAAEWDRVHPVH AGPIAPGQIREPRGSDIA GTTSNLQEQIGWMTHNPPIPVGEIYKKWIIMGLNKIVRMYSPVSILDIKQGPKEPFR DYVDRFYKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPAHKARVLAEAMSQ ATNSAAIMMQKGNFRNQRRTVKCFNCGKEGHIAKNCRAPRKKGCWKCGQEGHQMKDCNERQANFLGR SWPSLKGR PGNFLQNRPEPSAPPEESFKFGEETTTPPQKQEPIDKDLYPLASLRSLFGNDPSST SEQ ID NO: 787 CEN- 4 Preserved HIV B gag, Custom PIVQNMQGQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPPHDLNTMLNTIGGHQAAMQILKETINE EAAEWDRVHPVHAGPIAPGQIREPRGSDIAGTTSNLQEQIGWMTHNPPIPVGEIYKKWIIMGLNKIVRMYSPVSI LDIKQGPKEPFRDYVDRFYKTLRAEQAT QEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPA HKARVL SEQ ID NO: 788 HIV C gag CEN-5, Custom MGSRASVLSGGKLDKWEKIRLRPGGKKKYQLKHIVWASRELERYALNPGLLETAEGCRQILEQLQPALQTGSEEL RSLYNTVAVLYCVHQKIEVKDTKEALEKVEEEQNK SKKRIQQAQQAAAADTGNSSKVSQNYPIVRNLQGQMVHQP ISPRTLNAWVKVIEEKAFSPEVIPMFSALAEGATPQDLNLMLNAVGGHQAAMQMLKDTINEEAAEWDRMHPVHAG PVAPGQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRMYSPVSILDIKQGPKEPFRDY VDRFYRTL RAEQASQDVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPSHKARVLAEAMSQVT NSTAIMMQRGNFKNQRKIVKCFNCGKEGHIAKNCRAPRKRGCWKCGREGHQMKECTERQVNFLGKIWPSYKGRPG NFLQNRPEPTAPPAPPEESFRFGEGTTTPSQKQGTIDKELYPLTSLRSLFGNDPS SEQ ID NO: 7 89 CEN-5 Preserved HIV B gag, Custom PIVRNLQGQMVHQPISPRTLNAWVKVIEEKAFSPEVIPMFSALAEGATPQDLNLMLNAVGGHQAAMQMLKDTINE EAAEWDRMHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQIGWMTSNPPIPVGEIYKRWIIMGLNKIVRMYSPVSI LDIKQGPKEPFRDYVDRFYRTLRAEQASQDVKNWMTETLLVQNSNPDC KTILKALGPGATLEEMMTACQGVGGPS HKARVL SEQ ID NO: 790 VTSSNMNNA SEQ ID NO: 791 TSSNMNNAD SEQ ID NO: 792 TSSNMNNADSVWLRAQEEE SEQ ID NO: 793 TSSNMNNADCVWLRAQEEE SEQ ID NO: 794 ARCHSLM SEQ ID NO: 795 DEFGKLM SEQ ID NO: 796 EPTAPPAEPTAP SEQ ID NO : 797 PTAPPAEPTAPP SEQ ID NO: 798 EPTAPPAEPTAPP SEQ ID NO: 799 ARCGSLM SEQ ID NO: 800 ARCGSPM SEQ ID NO: 801 ARYGSLM SEQ ID NO: 802 AYCHSLM SEQ ID NO: 803 YRCHSLM SEQ ID NO: 804 DEFGSLM SEQ ID NO: 805 DEFGKLM SEQ ID NO: 806 ARCCDEGH SEQ ID NO: 807 ARCDEFGH SEQ ID NO: 808 ARCCDE-GH SEQ ID NO: 809 ARC-DEFGH SEQ ID NO: 810 DECHJLM SEQ ID NO: 811 DEFGJLM

Claims (18)

1. Vaccine against HIV-1 CHARACTERIZED by the fact that it comprises one or more vehicles encoding one or more antigens, wherein the antigen comprises the amino acid sequence selected from the group of SEQ ID NOs: 691 to 705, 707, 709, 711 , 717, 718, 720, 722, 724 and 726 to 789. 2. HIV-1 vaccine CHARACTERIZED by the fact that it comprises one or more carriers encoding one or more population episense antigens, wherein the population episense antigen comprises the amino acid sequence selected from the group of SEQ ID NOs: 691, 697 to 705, 707, 709, 711, 717, 718, 720, 722, 724, 726, 755, 766, 767, 778 and 779. 3. Vaccine, according to claim 1 or 2, CHARACTERIZED by the fact that: i) the vehicle is DNA, protein or a vector, ii) the vehicle is a viral vector or a bacterial vector, iii) the vehicle is a viral vector comprising a cytomegalovirus (CMV), poxvirus, adenovirus, rubella, sendai virus, rhabdovirus, alphavirus or adeno-associated virus backbone, or iv) the carrier is a human CMV (HCMV) backbone or a rhesus CMV backbone (RhCMV); in particular wherein: a) the CMV backbone is devoid of the UL130-128 gene region, b) the CMV backbone is devoid of the UL82 gene encoding the pp71 tegument protein, or c) the CMV backbone is devoid of the UL130-128 gene region and the UL82 gene that encodes the tegument protein pp71. 4. Vaccine, according to any one of claims 1 to 3, CHARACTERIZED by the fact that: i) the population episense antigen comprises epitopes of Gag, Pol, Nef, Env, Tat, Rev, Vpr, Vif or Vpu; ii) the population episense antigen comprises Gag epitopes, wherein the amino acid sequence of the population episense antigen comprises the amino acid sequence of SEQ ID NO: 697, SEQ ID NO: 698, SEQ ID NO: 699, or SEQ ID NO : 700; SEQ ID NO: 718, SEQ ID NO: 720, SEQ ID NO: 730, SEQ ID NO: 732, SEQ ID NO: 742 or SEQ ID NO: 744; iii) the population episense antigen comprises the amino acid sequence of SEQ ID NO: 731, SEQ ID NO: 733, SEQ ID NO: 743 or SEQ ID NO: 745; iv) the population episense antigen comprises the amino acid sequence of SEQ ID NO: 722, SEQ ID NO: 724, SEQ ID NO: 734, SEQ ID NO: 736, SEQ ID NO: 746, SEQ ID NO: 748; v) the population episense antigen comprises the amino acid sequence of SEQ ID NO: 735, SEQ ID NO: 737, SEQ ID NO: 747 or SEQ ID NO: 749; vi) the population episense antigen comprises the amino acid sequence of SEQ ID NO: 703, SEQ ID NO: 704, SEQ ID NO: 709, SEQ ID NO: 711, SEQ ID NO: 717, SEQ ID NO: 726, SEQ ID NO: 728, SEQ ID NO: 738, SEQ ID NO: 740, SEQ ID NO: 750 or SEQ ID NO: 752; or vii) the population episense antigen comprises the amino acid sequence of SEQ ID NO: 727, SEQ ID NO: 729, SEQ ID NO: 739, SEQ ID NO: 741, SEQ ID NO: 751 or SEQ ID NO: 753; in particular where: viii) the population episense antigen comprises epitopes from a conserved region of HIV; ix) the population episense antigen comprises epitopes from a conserved region of Gag, Pol or Nef; or x) the population episense antigen comprises epitopes from a conserved region of the Gag p24 capsid protein. 5. Vaccine according to any one of claims 1 to 4, CHARACTERIZED by the fact that the population episense antigen is a fusion antigen comprising two or more population episense antigens generated by the EpiGraph method; in particular wherein: i) the fusion antigen comprises a population episense antigen comprising Gag epitopes and a population episense antigen comprising Nef epitopes; ii) the fusion antigen comprises a population episense antigen comprising epitopes from a conserved region of Gag and a population episense antigen comprising epitopes from a conserved region of Nef; iii) the fusion antigen comprises a population episense antigen comprising epitopes from a conserved region of the p24 capsid protein of Gag and a population episense antigen comprising epitopes from a conserved region of Nef; or iv) the fusion antigen comprises the amino acid sequence of SEQ ID NO: 701, SEQ ID NO: 702, SEQ ID NO: 705, or SEQ ID NO: 707. 6. Vaccine, according to any one of claims 1 to 5, CHARACTERIZED by the fact that: i) the population episense antigen is essential for clade B of HIV-1 epidemic in the United States; ii) the population episense antigen is essential for the HIV-1 clade C epidemic in South Africa; iii) population episense antigen is essential for regional epidemic HIV-1 clade 2 in Thailand; or iv) the population episense antigen is essential for the global pool of HIV-1 group M. 7. Vaccine, according to claim 6, CHARACTERIZED by the fact that: i) the population episense antigen comprises Gag epitopes; ii) the population episense antigen comprises epitopes from a conserved region of Gag; iii) the population episense antigen comprises epitopes from a conserved region of the Gag p24 capsid protein; iv) the population episense antigen comprises Nef epitopes; v) the population episense antigen comprises epitopes from a conserved region of Nef; vi) the population episense antigen comprises Pol epitopes; or vii) the population episense antigen comprises epitopes from a conserved region of Pol; in particular wherein the population episense antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 703, 704, 709, 711, 717, 718, 720, 722, 724 and 726 to 753. 8. Vaccine according to claim 7, CHARACTERIZED by the fact that the population episense antigen is a fusion antigen comprising two or more population episense antigens, wherein: i) the fusion antigen comprises a population episense antigen population comprising Gag epitopes and a population episense antigen comprising Nef epitopes; ii) the fusion antigen comprises a population episense antigen comprising epitopes from a conserved region of Gag and a population episense antigen comprising epitopes from a conserved region of Nef; or iii) the fusion antigen comprises a population episense antigen comprising epitopes from a conserved region of the p24 capsid protein of Gag and a population episense antigen comprising epitopes from a conserved region of Nef; in particular wherein the fusion antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 701, 702, 705 and 707. 9. HIV-1 Vaccine CHARACTERIZED by the fact that it comprises one or more carriers and one or more population episense antigens determined using the EpiGraph approach. 10. Use of a vaccine, as defined in any one of claims 1 to 9, CHARACTERIZED by the fact that it is in the manufacture of a medicine to protect an individual from an HIV-1 infection or to treat HIV-1 in an individual in need for the same. 11. Vaccine, according to any one of claims 1 to 9, CHARACTERIZED by the fact that it additionally comprises one or more personalized antigens, wherein: i) the vehicle is DNA, protein or a vector, ii) the vehicle is a vector viral or a bacterial vector, iii) the carrier is a viral vector comprising a cytomegalovirus (CMV), poxvirus, adenovirus, rubella, sendai virus, rhabdovirus, alphavirus or adeno-associated virus backbone, or iv) the carrier is a backbone of human CMV (HCMV) or a backbone of rhesus CMV (RhCMV); in particular wherein: a) the CMV backbone is devoid of the UL130-128 gene region, b) the CMV backbone is devoid of the UL82 gene encoding the pp71 tegument protein, or c) the CMV backbone is devoid of the UL130-128 gene region and the UL82 gene that encodes the tegument protein pp71. 12. Vaccine, according to claim 11, CHARACTERIZED by the fact that: i) the personalized antigen comprises Gag epitopes; ii) the personalized antigen comprises Gag epitopes, wherein the amino acid sequence of the personalized antigen comprises the amino acid sequence of SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694, SEQ ID NO: 695 or SEQ ID NO: 696; iii) the vaccine comprises a first personalized antigen and a second personalized antigen, wherein the first personalized antigen and the second personalized antigen comprise two of the amino acid sequences of SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694 , SEQ ID NO: 695 and SEQ ID NO: 696; iv) the vaccine comprises a first personalized antigen, a second personalized antigen and a third personalized antigen, wherein the first personalized antigen, the second personalized antigen and the third personalized antigen comprise three of the amino acid sequences of: SEQ ID NO: 692, SEQ ID NO: 693, SEQ ID NO: 694, SEQ ID NO: 695 and SEQ ID NO: 696; or v) the personalized antigen comprises the amino acid sequence of an inactivated Gag protein, wherein the amino acid sequence of the inactivated Gag protein has been inactivated by eliminating a myristoylation sequence at the N-terminus of the Gag protein; in particular wherein: vi) the population episense antigen comprises Gag epitopes; vii) the population episense antigen comprises Gag epitopes, wherein the amino acid sequence of the population episense antigen comprises the amino acid sequence of SEQ ID NO: 691; or viii) the population episense antigen comprises the amino acid sequence of an inactivated Gag protein, wherein the amino acid sequence of the inactivated Gag protein has been inactivated by eliminating a myristoylation sequence at the N-terminus of the Gag protein. 13. Vaccine, according to claim 11 or 12, CHARACTERIZED by the fact that: i) the population episense antigen is essential for the global pool of HIV-1 group M; ii) the population episense antigen is essential for the HIV-1 clade C epidemic in South Africa; iii) population episense antigen is essential for HIV-1 clade B epidemic in South Africa; or iv) population episense antigen is essential for regional epidemic HIV-1 clade 2 in Thailand; wherein: v) the population episense antigen and the personalized antigen comprise Gag epitopes; vi) the population episense antigen and the personalized antigen comprise epitopes from a conserved region of Gag; vii) the population episense antigen and the personalized antigen comprise epitopes from a conserved region of the Gag p24 capsid protein; viii) the population episense antigen and the personalized antigen comprise Nef epitopes; or ix) the population episense antigen and the personalized antigen comprise Pol epitopes; in particular wherein: a) the population episense antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 754 to 755, 766 to 767 and 778 to 779; b) the population episense antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 754 to 755, 766 to 767 and 778 to 779 and the personalized antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 756 to 765, 768 to 777 and 780 to 789; c) the vaccine comprises a first personalized antigen and a second personalized antigen, wherein the population episense antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 754 to 755, 766 to 767 and 778 to 779, and wherein the first personalized antigen and the second personalized antigen comprise two of the amino acid sequences selected from the group consisting of SEQ ID NOs: 756 to 765, 768 to 777 and 780 to 789; or d) the vaccine comprises a first personalized antigen, a second personalized antigen and a third personalized antigen, wherein the population episense antigen comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 754 to 755, 766 to 767 and 778 to 779, and wherein the first personalized antigen, the second personalized antigen and the third personalized antigen comprise three of the amino acid sequences selected from the group consisting of SEQ ID NOs: 756 to 765, 768 to 777 and 780 to 789. 14. Vaccine, according to any one of claims 11 to 13, CHARACTERIZED by the fact that it further comprises: i) an HCMV vector comprising an HCMV backbone and a personalized antigen selected to be an HIV-1 strain of better natural matching; or ii) an HCMV vector comprising an HCMV backbone and a custom antigen selected to be a different (and distant) best match HIV-1 strain. 15. Use of a vaccine, as defined in any one of claims 11 to 14, CHARACTERIZED by the fact that it is in the manufacture of a medicine to treat HIV-1 in an individual in need thereof. 16. Method for designing and producing an HIV-1 vaccine for an individual comprising: (a) designing EpiGraph vaccine antigens to ideally cover diversity within a geographic area using a vaccine antigen amino acid sequence generated using the EpiGraph antigen amino acid sequence selection method; and (b) producing said designed EpiGraph vaccine antigens; in particular wherein the method further comprises the steps of determining the amino acid sequence of HIV-1 virus in an individual and inserting the EpiGraph vaccine antigens into a vector. 17. Use of a vaccine CHARACTERIZED by the fact that it is in the manufacture of a drug to induce an effector memory T cell response, wherein the vaccine comprises one or more EpiGraph vaccine antigens and a vector, wherein the vaccine antigen EpiGraph comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 691 to 705, 707, 709, 711, 712, 717, 718, 720, 722, 724 and 726 to 789. 18. Polypeptide CHARACTERIZED by the fact that it comprises (i) one or more HIV-1 population episense antigens determined using the EpiGraph approach or personalized HIV-1 antigens, and/or (ii) an amino acid sequence selected from the group which consists of SEQ ID NOs: 691 to 705, 707, 709, 711, 712, 717, 718, 720, 722, 724 and 726 to 789.